PDB Short entry for 5Y0O HEADER LIGASE 18-JUL-17 5Y0O TITLE CRYSTAL STRUCTURE OF APO BSTMCAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0348 PROTEIN B4417_3650; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE GENE WAS CLONED INTO PET15B WITH NDEI AND XHOI COMPND 6 SITE, AND EXPRESSED AS A N-TERMINALLY HIS-TAGGED PROTEIN. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: B4417_3650; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACETATE LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YAMASHITA,K.TOMITA REVDAT 3 22-NOV-23 5Y0O 1 REMARK REVDAT 2 26-DEC-18 5Y0O 1 HEADER KEYWDS JRNL REVDAT 1 18-JUL-18 5Y0O 0 JRNL AUTH T.TANIGUCHI,K.MIYAUCHI,Y.SAKAGUCHI,S.YAMASHITA,A.SOMA, JRNL AUTH 2 K.TOMITA,T.SUZUKI JRNL TITL ACETATE-DEPENDENT TRNA ACETYLATION REQUIRED FOR DECODING JRNL TITL 2 FIDELITY IN PROTEIN SYNTHESIS. JRNL REF NAT. CHEM. BIOL. V. 14 1010 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 30150682 JRNL DOI 10.1038/S41589-018-0119-Z REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2203 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.7483 - 5.7941 0.95 2817 149 0.1216 0.1721 REMARK 3 2 5.7941 - 4.6000 0.95 2674 141 0.1308 0.1461 REMARK 3 3 4.6000 - 4.0189 0.95 2650 139 0.1321 0.1736 REMARK 3 4 4.0189 - 3.6516 0.95 2640 139 0.1635 0.2111 REMARK 3 5 3.6516 - 3.3899 0.95 2584 136 0.1854 0.2140 REMARK 3 6 3.3899 - 3.1901 0.95 2620 138 0.2103 0.2895 REMARK 3 7 3.1901 - 3.0303 0.95 2604 137 0.2285 0.3040 REMARK 3 8 3.0303 - 2.8984 0.95 2599 137 0.2425 0.2866 REMARK 3 9 2.8984 - 2.7869 0.95 2570 135 0.2612 0.3201 REMARK 3 10 2.7869 - 2.6907 0.95 2582 136 0.2658 0.3128 REMARK 3 11 2.6907 - 2.6066 0.95 2549 134 0.2784 0.3419 REMARK 3 12 2.6066 - 2.5321 0.95 2624 138 0.2982 0.3356 REMARK 3 13 2.5321 - 2.4654 0.95 2556 135 0.3146 0.3493 REMARK 3 14 2.4654 - 2.4053 0.95 2548 134 0.3297 0.3980 REMARK 3 15 2.4053 - 2.3506 0.95 2572 135 0.3564 0.3650 REMARK 3 16 2.3506 - 2.3006 0.95 2593 137 0.3742 0.4083 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.5100 REMARK 3 OPERATOR: -K,-H,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 6756 REMARK 3 ANGLE : 1.233 9134 REMARK 3 CHIRALITY : 0.047 1010 REMARK 3 PLANARITY : 0.005 1166 REMARK 3 DIHEDRAL : 16.953 2530 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:105) REMARK 3 ORIGIN FOR THE GROUP (A): 17.4829 -7.2938 -56.8066 REMARK 3 T TENSOR REMARK 3 T11: 0.6800 T22: 0.4774 REMARK 3 T33: 0.3562 T12: 0.0488 REMARK 3 T13: 0.0047 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 3.4077 L22: 1.7883 REMARK 3 L33: 3.8588 L12: -0.5443 REMARK 3 L13: 0.9365 L23: 1.2885 REMARK 3 S TENSOR REMARK 3 S11: -0.0832 S12: 0.4190 S13: 0.0961 REMARK 3 S21: -0.5584 S22: -0.0627 S23: 0.1026 REMARK 3 S31: -0.7139 S32: -0.0126 S33: 0.1297 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 106:153) REMARK 3 ORIGIN FOR THE GROUP (A): 45.4800 -2.3670 -63.0111 REMARK 3 T TENSOR REMARK 3 T11: 0.9124 T22: 0.4792 REMARK 3 T33: 0.5553 T12: 0.0903 REMARK 3 T13: 0.0992 T23: 0.0550 REMARK 3 L TENSOR REMARK 3 L11: 5.0093 L22: 3.7748 REMARK 3 L33: 8.2326 L12: 2.2559 REMARK 3 L13: 2.2217 L23: 2.9895 REMARK 3 S TENSOR REMARK 3 S11: 0.3194 S12: 0.5598 S13: -0.2501 REMARK 3 S21: -0.2878 S22: 0.1777 S23: -0.7020 REMARK 3 S31: 1.9802 S32: 0.6656 S33: -0.5971 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 154:414) REMARK 3 ORIGIN FOR THE GROUP (A): 20.1042 -4.5913 -45.8152 REMARK 3 T TENSOR REMARK 3 T11: 0.6245 T22: 0.4029 REMARK 3 T33: 0.3602 T12: 0.0157 REMARK 3 T13: 0.0284 T23: 0.0578 REMARK 3 L TENSOR REMARK 3 L11: 1.6249 L22: 0.9512 REMARK 3 L33: 3.3431 L12: 0.1039 REMARK 3 L13: 0.3901 L23: 1.0744 REMARK 3 S TENSOR REMARK 3 S11: -0.1082 S12: 0.2004 S13: 0.1785 REMARK 3 S21: -0.3747 S22: 0.0296 S23: 0.1144 REMARK 3 S31: -0.9032 S32: -0.0514 S33: 0.0668 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 1:105) REMARK 3 ORIGIN FOR THE GROUP (A): 23.8912 -0.9074 4.1939 REMARK 3 T TENSOR REMARK 3 T11: 0.5301 T22: 0.7140 REMARK 3 T33: 0.3135 T12: 0.1580 REMARK 3 T13: 0.0051 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 2.2573 L22: 2.9839 REMARK 3 L33: 3.8439 L12: -0.5433 REMARK 3 L13: 0.5877 L23: 1.3503 REMARK 3 S TENSOR REMARK 3 S11: -0.0781 S12: -0.5702 S13: 0.1518 REMARK 3 S21: 0.2195 S22: -0.1145 S23: -0.0370 REMARK 3 S31: -0.6150 S32: -1.2159 S33: 0.1643 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 106:153) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4957 -29.0524 10.1751 REMARK 3 T TENSOR REMARK 3 T11: 0.5798 T22: 0.8098 REMARK 3 T33: 0.6848 T12: 0.2173 REMARK 3 T13: -0.1086 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 3.3038 L22: 6.6118 REMARK 3 L33: 6.9151 L12: 2.2816 REMARK 3 L13: 1.1241 L23: 3.1051 REMARK 3 S TENSOR REMARK 3 S11: 0.3579 S12: 0.0193 S13: -1.0417 REMARK 3 S21: 1.0941 S22: 0.4327 S23: -0.9301 REMARK 3 S31: 1.0654 S32: 1.5696 S33: -0.5957 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 154:414) REMARK 3 ORIGIN FOR THE GROUP (A): 21.2908 -3.5642 -6.8017 REMARK 3 T TENSOR REMARK 3 T11: 0.4431 T22: 0.6151 REMARK 3 T33: 0.3520 T12: 0.0922 REMARK 3 T13: -0.0005 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 1.5040 L22: 1.3916 REMARK 3 L33: 4.0931 L12: 0.2026 REMARK 3 L13: 0.9079 L23: 0.1215 REMARK 3 S TENSOR REMARK 3 S11: -0.0946 S12: -0.3948 S13: 0.0702 REMARK 3 S21: 0.0949 S22: 0.0051 S23: -0.0038 REMARK 3 S31: -0.3499 S32: -1.0662 S33: 0.0982 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Y0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300002650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43997 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.24 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 13.21 REMARK 200 R MERGE FOR SHELL (I) : 1.55700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5Y0N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, PEG400, KCL, MGCL2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 33.87750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 105.40250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.82800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 105.40250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.87750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.82800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 VAL A 415 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 VAL B 415 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN A 11 NH1 ARG A 211 1.93 REMARK 500 O TYR B 10 NH1 ARG B 55 2.01 REMARK 500 O ALA B 48 OH TYR B 381 2.06 REMARK 500 OE2 GLU B 387 OG1 THR B 391 2.06 REMARK 500 O GLY A 39 NH2 ARG A 55 2.07 REMARK 500 NZ LYS B 78 OD1 ASP B 80 2.09 REMARK 500 O THR B 246 OG SER B 249 2.11 REMARK 500 O ARG A 279 OG SER A 283 2.13 REMARK 500 OE2 GLU A 387 OG1 THR A 391 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER B 137 O LEU B 355 4445 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 198 C - N - CA ANGL. DEV. = 10.5 DEGREES REMARK 500 LEU B 150 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 150 -17.05 79.30 REMARK 500 ALA A 155 -120.11 51.43 REMARK 500 LEU A 156 77.10 57.35 REMARK 500 LYS A 160 74.64 -151.23 REMARK 500 PRO A 161 44.09 -72.95 REMARK 500 SER A 189 -132.59 59.56 REMARK 500 SER A 190 109.90 -42.33 REMARK 500 ASP A 191 -133.14 37.15 REMARK 500 ASP A 194 -135.36 64.99 REMARK 500 ALA A 195 -143.43 48.84 REMARK 500 PRO A 198 -173.96 -63.00 REMARK 500 ILE A 204 72.86 63.22 REMARK 500 SER A 240 -73.37 -55.02 REMARK 500 SER A 361 -62.05 -104.16 REMARK 500 HIS A 368 141.03 -174.46 REMARK 500 PRO A 388 35.97 -90.72 REMARK 500 TYR A 398 -69.39 -98.53 REMARK 500 GLN A 410 73.32 48.48 REMARK 500 LEU B 150 -17.42 76.36 REMARK 500 ALA B 155 -124.77 53.77 REMARK 500 LEU B 156 74.69 59.92 REMARK 500 LYS B 160 66.41 -154.28 REMARK 500 PRO B 161 48.78 -68.12 REMARK 500 SER B 189 -140.72 59.80 REMARK 500 SER B 190 109.64 -45.73 REMARK 500 ASP B 191 -134.70 39.38 REMARK 500 TYR B 192 -60.66 -126.12 REMARK 500 ASP B 194 -129.29 61.99 REMARK 500 ALA B 195 -138.44 58.69 REMARK 500 PRO B 198 -176.81 -59.40 REMARK 500 ILE B 204 75.29 59.89 REMARK 500 HIS B 368 137.17 -173.24 REMARK 500 PRO B 388 45.92 -90.87 REMARK 500 GLN B 410 70.76 56.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 158 SER A 159 149.26 REMARK 500 LYS A 160 PRO A 161 -146.86 REMARK 500 PRO A 161 ASN A 162 141.15 REMARK 500 SER A 189 SER A 190 -120.80 REMARK 500 ASP A 408 GLU A 409 -123.64 REMARK 500 LYS B 160 PRO B 161 -146.69 REMARK 500 SER B 189 SER B 190 -124.72 REMARK 500 ASP B 408 GLU B 409 -135.47 REMARK 500 REMARK 500 REMARK: NULL DBREF1 5Y0O A 1 415 UNP A0A164SIT4_BACIU DBREF2 5Y0O A A0A164SIT4 1 415 DBREF1 5Y0O B 1 415 UNP A0A164SIT4_BACIU DBREF2 5Y0O B A0A164SIT4 1 415 SEQADV 5Y0O MET A -19 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O GLY A -18 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER A -17 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER A -16 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS A -15 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS A -14 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS A -13 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS A -12 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS A -11 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS A -10 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER A -9 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER A -8 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O GLY A -7 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O LEU A -6 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O VAL A -5 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O PRO A -4 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O ARG A -3 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O GLY A -2 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER A -1 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS A 0 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O MET B -19 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O GLY B -18 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER B -17 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER B -16 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS B -15 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS B -14 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS B -13 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS B -12 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS B -11 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS B -10 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER B -9 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER B -8 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O GLY B -7 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O LEU B -6 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O VAL B -5 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O PRO B -4 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O ARG B -3 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O GLY B -2 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O SER B -1 UNP A0A164SIT EXPRESSION TAG SEQADV 5Y0O HIS B 0 UNP A0A164SIT EXPRESSION TAG SEQRES 1 A 435 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 435 LEU VAL PRO ARG GLY SER HIS MET LYS ALA VAL GLY LEU SEQRES 3 A 435 VAL VAL GLU TYR ASN PRO PHE HIS ASN GLY HIS LEU TYR SEQRES 4 A 435 HIS ALA GLN THR ALA LYS LEU GLN THR GLY CYS ASP THR SEQRES 5 A 435 ALA VAL ALA VAL MET SER GLY HIS PHE LEU GLN ARG GLY SEQRES 6 A 435 GLU PRO ALA VAL VAL SER LYS TRP ALA ARG THR LYS MET SEQRES 7 A 435 ALA LEU GLN SER GLY VAL ASP LEU VAL ILE GLU LEU PRO SEQRES 8 A 435 TYR LEU TYR ALA VAL GLN LYS ALA ASP ILE PHE ALA ARG SEQRES 9 A 435 GLY SER VAL SER ILE LEU ASN GLU LEU GLU CYS GLU ALA SEQRES 10 A 435 LEU PHE PHE GLY SER GLU ASN GLY ASP ILE LYS PRO PHE SEQRES 11 A 435 LEU GLU THR ALA GLN LEU ILE ASP GLU HIS LYS HIS ILE SEQRES 12 A 435 LEU ASN ASP ARG ILE LYS GLU GLU LEU LYS LYS GLY ALA SEQRES 13 A 435 SER TYR PRO ALA ALA ALA ALA ILE ALA PHE SER SER ILE SEQRES 14 A 435 LEU HIS THR GLU SER ALA LEU ASP LEU SER LYS PRO ASN SEQRES 15 A 435 ASN ILE LEU GLY TYR GLN TYR VAL THR SER ILE LEU THR SEQRES 16 A 435 GLY GLY TYR PRO MET LYS PRO TYR THR THR ALA ARG ILE SEQRES 17 A 435 SER SER ASP TYR HIS ASP ALA ASP LEU PRO GLU GLY GLU SEQRES 18 A 435 ASN HIS ILE ALA SER ALA THR SER ILE ARG LYS ALA MET SEQRES 19 A 435 ILE GLY GLN ASN LEU GLU ALA CYS LEU ARG PHE LEU PRO SEQRES 20 A 435 ALA ALA SER ALA ARG GLU LEU ALA ALA TYR ARG LYS SER SEQRES 21 A 435 PHE GLY LEU TRP HIS THR PRO GLU SER TYR PHE SER TYR SEQRES 22 A 435 LEU LYS TYR SER LEU SER THR VAL THR ALA ARG GLU LEU SEQRES 23 A 435 GLN GLN VAL TYR GLU VAL GLU GLU GLY LEU GLU HIS ARG SEQRES 24 A 435 ILE ILE ARG SER ILE ARG LYS SER SER SER TYR GLN GLU SEQRES 25 A 435 PHE MET GLU LEU LEU LYS THR LYS ARG TYR THR TRP THR SEQRES 26 A 435 ARG LEU GLN ARG MET ASN THR HIS ILE LEU THR ARG THR SEQRES 27 A 435 LYS LYS GLN ASP MET GLN LYS LEU LEU ASP ASN ASP LYS SEQRES 28 A 435 ALA PRO TYR ILE ARG LEU LEU GLY MET THR LYS LYS GLY SEQRES 29 A 435 GLN ALA TYR LEU SER GLU LYS LYS LYS ALA LEU SER VAL SEQRES 30 A 435 PRO LEU VAL SER LYS LEU SER SER PHE SER HIS PRO ALA SEQRES 31 A 435 LEU ASP LEU ASP VAL LYS ALA SER ARG ILE TYR SER LEU SEQRES 32 A 435 PRO ILE GLU GLU PRO LEU ARG THR GLU PHE ASP LEU GLN SEQRES 33 A 435 GLU TYR GLY HIS ALA PRO ILE ARG TYR ASP GLU ASP GLU SEQRES 34 A 435 GLN HIS PHE LEU ASN VAL SEQRES 1 B 435 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 435 LEU VAL PRO ARG GLY SER HIS MET LYS ALA VAL GLY LEU SEQRES 3 B 435 VAL VAL GLU TYR ASN PRO PHE HIS ASN GLY HIS LEU TYR SEQRES 4 B 435 HIS ALA GLN THR ALA LYS LEU GLN THR GLY CYS ASP THR SEQRES 5 B 435 ALA VAL ALA VAL MET SER GLY HIS PHE LEU GLN ARG GLY SEQRES 6 B 435 GLU PRO ALA VAL VAL SER LYS TRP ALA ARG THR LYS MET SEQRES 7 B 435 ALA LEU GLN SER GLY VAL ASP LEU VAL ILE GLU LEU PRO SEQRES 8 B 435 TYR LEU TYR ALA VAL GLN LYS ALA ASP ILE PHE ALA ARG SEQRES 9 B 435 GLY SER VAL SER ILE LEU ASN GLU LEU GLU CYS GLU ALA SEQRES 10 B 435 LEU PHE PHE GLY SER GLU ASN GLY ASP ILE LYS PRO PHE SEQRES 11 B 435 LEU GLU THR ALA GLN LEU ILE ASP GLU HIS LYS HIS ILE SEQRES 12 B 435 LEU ASN ASP ARG ILE LYS GLU GLU LEU LYS LYS GLY ALA SEQRES 13 B 435 SER TYR PRO ALA ALA ALA ALA ILE ALA PHE SER SER ILE SEQRES 14 B 435 LEU HIS THR GLU SER ALA LEU ASP LEU SER LYS PRO ASN SEQRES 15 B 435 ASN ILE LEU GLY TYR GLN TYR VAL THR SER ILE LEU THR SEQRES 16 B 435 GLY GLY TYR PRO MET LYS PRO TYR THR THR ALA ARG ILE SEQRES 17 B 435 SER SER ASP TYR HIS ASP ALA ASP LEU PRO GLU GLY GLU SEQRES 18 B 435 ASN HIS ILE ALA SER ALA THR SER ILE ARG LYS ALA MET SEQRES 19 B 435 ILE GLY GLN ASN LEU GLU ALA CYS LEU ARG PHE LEU PRO SEQRES 20 B 435 ALA ALA SER ALA ARG GLU LEU ALA ALA TYR ARG LYS SER SEQRES 21 B 435 PHE GLY LEU TRP HIS THR PRO GLU SER TYR PHE SER TYR SEQRES 22 B 435 LEU LYS TYR SER LEU SER THR VAL THR ALA ARG GLU LEU SEQRES 23 B 435 GLN GLN VAL TYR GLU VAL GLU GLU GLY LEU GLU HIS ARG SEQRES 24 B 435 ILE ILE ARG SER ILE ARG LYS SER SER SER TYR GLN GLU SEQRES 25 B 435 PHE MET GLU LEU LEU LYS THR LYS ARG TYR THR TRP THR SEQRES 26 B 435 ARG LEU GLN ARG MET ASN THR HIS ILE LEU THR ARG THR SEQRES 27 B 435 LYS LYS GLN ASP MET GLN LYS LEU LEU ASP ASN ASP LYS SEQRES 28 B 435 ALA PRO TYR ILE ARG LEU LEU GLY MET THR LYS LYS GLY SEQRES 29 B 435 GLN ALA TYR LEU SER GLU LYS LYS LYS ALA LEU SER VAL SEQRES 30 B 435 PRO LEU VAL SER LYS LEU SER SER PHE SER HIS PRO ALA SEQRES 31 B 435 LEU ASP LEU ASP VAL LYS ALA SER ARG ILE TYR SER LEU SEQRES 32 B 435 PRO ILE GLU GLU PRO LEU ARG THR GLU PHE ASP LEU GLN SEQRES 33 B 435 GLU TYR GLY HIS ALA PRO ILE ARG TYR ASP GLU ASP GLU SEQRES 34 B 435 GLN HIS PHE LEU ASN VAL FORMUL 3 HOH *57(H2 O) HELIX 1 AA1 HIS A 14 GLY A 29 1 16 HELIX 2 AA2 SER A 51 SER A 62 1 12 HELIX 3 AA3 PRO A 71 VAL A 76 1 6 HELIX 4 AA4 LYS A 78 LEU A 93 1 16 HELIX 5 AA5 ASP A 106 LYS A 133 1 28 HELIX 6 AA6 SER A 137 ILE A 149 1 13 HELIX 7 AA7 ASN A 162 GLY A 177 1 16 HELIX 8 AA8 SER A 206 ILE A 215 1 10 HELIX 9 AA9 CYS A 222 LEU A 226 5 5 HELIX 10 AB1 PRO A 227 PHE A 241 1 15 HELIX 11 AB2 THR A 246 SER A 249 5 4 HELIX 12 AB3 TYR A 250 THR A 260 1 11 HELIX 13 AB4 THR A 262 GLN A 268 1 7 HELIX 14 AB5 GLY A 275 LYS A 286 1 12 HELIX 15 AB6 SER A 289 LYS A 298 1 10 HELIX 16 AB7 THR A 303 ARG A 317 1 15 HELIX 17 AB8 LYS A 319 ASP A 328 1 10 HELIX 18 AB9 THR A 341 LYS A 352 1 12 HELIX 19 AC1 LYS A 353 LEU A 355 5 3 HELIX 20 AC2 LYS A 362 PHE A 366 5 5 HELIX 21 AC3 HIS A 368 SER A 382 1 15 HELIX 22 AC4 PRO A 388 LEU A 395 1 8 HELIX 23 AC5 GLN A 396 TYR A 398 5 3 HELIX 24 AC6 HIS B 14 GLY B 29 1 16 HELIX 25 AC7 SER B 51 GLN B 61 1 11 HELIX 26 AC8 PRO B 71 VAL B 76 1 6 HELIX 27 AC9 LYS B 78 LEU B 93 1 16 HELIX 28 AD1 ILE B 107 LYS B 133 1 27 HELIX 29 AD2 SER B 137 SER B 148 1 12 HELIX 30 AD3 PRO B 161 GLY B 177 1 17 HELIX 31 AD4 SER B 206 GLY B 216 1 11 HELIX 32 AD5 LEU B 219 LEU B 226 5 8 HELIX 33 AD6 PRO B 227 GLY B 242 1 16 HELIX 34 AD7 THR B 246 SER B 249 5 4 HELIX 35 AD8 TYR B 250 THR B 260 1 11 HELIX 36 AD9 THR B 262 GLN B 268 1 7 HELIX 37 AE1 LEU B 276 LYS B 286 1 11 HELIX 38 AE2 SER B 289 LYS B 298 1 10 HELIX 39 AE3 THR B 303 ARG B 317 1 15 HELIX 40 AE4 LYS B 319 ASN B 329 1 11 HELIX 41 AE5 THR B 341 LYS B 352 1 12 HELIX 42 AE6 LYS B 353 LEU B 355 5 3 HELIX 43 AE7 HIS B 368 SER B 382 1 15 HELIX 44 AE8 LEU B 389 LEU B 395 1 7 HELIX 45 AE9 LEU B 395 HIS B 400 1 6 SHEET 1 AA1 7 LYS A 181 ALA A 186 0 SHEET 2 AA1 7 ALA A 97 SER A 102 1 N LEU A 98 O TYR A 183 SHEET 3 AA1 7 ALA A 3 VAL A 8 1 N GLY A 5 O ALA A 97 SHEET 4 AA1 7 THR A 32 SER A 38 1 O THR A 32 N VAL A 4 SHEET 5 AA1 7 LEU A 66 LEU A 70 1 O LEU A 70 N MET A 37 SHEET 6 AA1 7 ILE A 335 MET A 340 -1 O ARG A 336 N GLU A 69 SHEET 7 AA1 7 LEU A 359 VAL A 360 1 O VAL A 360 N ILE A 335 SHEET 1 AA2 8 LYS A 181 ALA A 186 0 SHEET 2 AA2 8 ALA A 97 SER A 102 1 N LEU A 98 O TYR A 183 SHEET 3 AA2 8 ALA A 3 VAL A 8 1 N GLY A 5 O ALA A 97 SHEET 4 AA2 8 THR A 32 SER A 38 1 O THR A 32 N VAL A 4 SHEET 5 AA2 8 LEU A 66 LEU A 70 1 O LEU A 70 N MET A 37 SHEET 6 AA2 8 ILE A 335 MET A 340 -1 O ARG A 336 N GLU A 69 SHEET 7 AA2 8 ILE A 403 ASP A 406 1 O ILE A 403 N MET A 340 SHEET 8 AA2 8 HIS A 411 PHE A 412 -1 O HIS A 411 N ASP A 406 SHEET 1 AA3 7 LYS B 181 ALA B 186 0 SHEET 2 AA3 7 ALA B 97 SER B 102 1 N PHE B 100 O TYR B 183 SHEET 3 AA3 7 ALA B 3 VAL B 8 1 N GLY B 5 O ALA B 97 SHEET 4 AA3 7 THR B 32 SER B 38 1 O THR B 32 N VAL B 4 SHEET 5 AA3 7 LEU B 66 LEU B 70 1 O LEU B 66 N ALA B 35 SHEET 6 AA3 7 ILE B 335 MET B 340 -1 O GLY B 339 N VAL B 67 SHEET 7 AA3 7 LEU B 359 VAL B 360 1 O VAL B 360 N ILE B 335 SHEET 1 AA4 8 LYS B 181 ALA B 186 0 SHEET 2 AA4 8 ALA B 97 SER B 102 1 N PHE B 100 O TYR B 183 SHEET 3 AA4 8 ALA B 3 VAL B 8 1 N GLY B 5 O ALA B 97 SHEET 4 AA4 8 THR B 32 SER B 38 1 O THR B 32 N VAL B 4 SHEET 5 AA4 8 LEU B 66 LEU B 70 1 O LEU B 66 N ALA B 35 SHEET 6 AA4 8 ILE B 335 MET B 340 -1 O GLY B 339 N VAL B 67 SHEET 7 AA4 8 ILE B 403 ASP B 406 1 O TYR B 405 N MET B 340 SHEET 8 AA4 8 HIS B 411 PHE B 412 -1 O HIS B 411 N ASP B 406 CISPEP 1 ASN A 11 PRO A 12 0 -2.49 CISPEP 2 GLU A 387 PRO A 388 0 -6.19 CISPEP 3 ASN B 11 PRO B 12 0 -3.16 CISPEP 4 GLU B 387 PRO B 388 0 -8.48 CRYST1 67.755 67.656 210.805 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014759 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004744 0.00000