PDB Short entry for 6N6K HEADER RNA BINDING PROTEIN/RNA 26-NOV-18 6N6K TITLE HUMAN REXO2 BOUND TO PAG COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA EXONUCLEASE 2 HOMOLOG,SMALL FRAGMENT NUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: OLIGORIBONUCLEASE, MITOCHONDRIAL, REXO2; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(P*AP*G)-3'); COMPND 9 CHAIN: D, C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: REXO2, SFN, SMFN, CGI-114; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS 3'-5' EXORIBONUCLEASE, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.D.LORMAND,H.SONDERMANN REVDAT 4 11-OCT-23 6N6K 1 LINK REVDAT 3 01-JAN-20 6N6K 1 REMARK REVDAT 2 16-OCT-19 6N6K 1 JRNL REVDAT 1 12-JUN-19 6N6K 0 JRNL AUTH S.K.KIM,J.D.LORMAND,C.A.WEISS,K.A.EGER,H.TURDIEV,A.TURDIEV, JRNL AUTH 2 W.C.WINKLER,H.SONDERMANN,V.T.LEE JRNL TITL A DEDICATED DIRIBONUCLEOTIDASE RESOLVES A KEY BOTTLENECK FOR JRNL TITL 2 THE TERMINAL STEP OF RNA DEGRADATION. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31225796 JRNL DOI 10.7554/ELIFE.46313 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 95173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.490 REMARK 3 FREE R VALUE TEST SET COUNT : 2372 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 26.3883 - 3.6428 1.00 5818 149 0.1399 0.1369 REMARK 3 2 3.6428 - 2.8926 1.00 5567 142 0.1388 0.1709 REMARK 3 3 2.8926 - 2.5272 1.00 5522 142 0.1552 0.1740 REMARK 3 4 2.5272 - 2.2963 1.00 5502 140 0.1520 0.1944 REMARK 3 5 2.2963 - 2.1318 1.00 5489 141 0.1506 0.1838 REMARK 3 6 2.1318 - 2.0062 1.00 5440 137 0.1489 0.1865 REMARK 3 7 2.0062 - 1.9057 1.00 5448 140 0.1558 0.1755 REMARK 3 8 1.9057 - 1.8228 1.00 5435 140 0.1516 0.1491 REMARK 3 9 1.8228 - 1.7526 1.00 5436 138 0.1502 0.1716 REMARK 3 10 1.7526 - 1.6922 1.00 5429 140 0.1543 0.1531 REMARK 3 11 1.6922 - 1.6393 1.00 5402 136 0.1577 0.1888 REMARK 3 12 1.6393 - 1.5924 1.00 5426 139 0.1610 0.1513 REMARK 3 13 1.5924 - 1.5505 1.00 5438 138 0.1726 0.1986 REMARK 3 14 1.5505 - 1.5127 1.00 5402 140 0.1803 0.2202 REMARK 3 15 1.5127 - 1.4783 1.00 5354 138 0.1940 0.1991 REMARK 3 16 1.4783 - 1.4468 1.00 5443 136 0.2125 0.2281 REMARK 3 17 1.4468 - 1.4179 0.97 5250 136 0.2525 0.2629 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.79 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: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 4:86) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9435 8.2139 12.8750 REMARK 3 T TENSOR REMARK 3 T11: 0.1046 T22: 0.1050 REMARK 3 T33: 0.0687 T12: -0.0067 REMARK 3 T13: 0.0022 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 2.1892 L22: 2.0101 REMARK 3 L33: 0.7400 L12: 0.5218 REMARK 3 L13: 0.3443 L23: 0.0913 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: 0.0160 S13: 0.0396 REMARK 3 S21: -0.1077 S22: -0.0072 S23: 0.0822 REMARK 3 S31: 0.0584 S32: -0.0378 S33: -0.0306 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 87:184) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8861 18.1601 15.6036 REMARK 3 T TENSOR REMARK 3 T11: 0.0995 T22: 0.1310 REMARK 3 T33: 0.1026 T12: -0.0018 REMARK 3 T13: 0.0054 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.3058 L22: 2.0435 REMARK 3 L33: 0.5641 L12: 0.2268 REMARK 3 L13: -0.2015 L23: -0.5295 REMARK 3 S TENSOR REMARK 3 S11: 0.0087 S12: 0.0137 S13: 0.0032 REMARK 3 S21: -0.1283 S22: 0.0036 S23: -0.0527 REMARK 3 S31: 0.0191 S32: 0.0157 S33: -0.0099 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 185:198) REMARK 3 ORIGIN FOR THE GROUP (A): 33.3210 31.1890 9.0462 REMARK 3 T TENSOR REMARK 3 T11: 0.5863 T22: 0.8693 REMARK 3 T33: 0.9729 T12: -0.0100 REMARK 3 T13: 0.0920 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 0.9220 L22: 9.8212 REMARK 3 L33: 8.4740 L12: 0.0787 REMARK 3 L13: 2.7567 L23: -1.2450 REMARK 3 S TENSOR REMARK 3 S11: 0.2422 S12: 0.3959 S13: 0.1937 REMARK 3 S21: -0.9056 S22: -0.4501 S23: -1.0711 REMARK 3 S31: 0.1894 S32: 1.1435 S33: 0.2353 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 2:7) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1179 43.1315 13.9836 REMARK 3 T TENSOR REMARK 3 T11: 0.5567 T22: 0.4316 REMARK 3 T33: 0.5379 T12: 0.1200 REMARK 3 T13: 0.0045 T23: 0.1648 REMARK 3 L TENSOR REMARK 3 L11: 3.7658 L22: 4.2988 REMARK 3 L33: 6.4779 L12: 0.9157 REMARK 3 L13: 2.4169 L23: -3.8926 REMARK 3 S TENSOR REMARK 3 S11: 0.3656 S12: 1.9715 S13: 1.7312 REMARK 3 S21: -1.5385 S22: -0.1058 S23: 0.4346 REMARK 3 S31: -1.8656 S32: -0.8506 S33: -0.2807 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 8:154) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8101 27.8698 32.3195 REMARK 3 T TENSOR REMARK 3 T11: 0.0915 T22: 0.1186 REMARK 3 T33: 0.0938 T12: -0.0154 REMARK 3 T13: -0.0015 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.0620 L22: 0.8272 REMARK 3 L33: 0.7586 L12: -0.1756 REMARK 3 L13: -0.1778 L23: 0.3368 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: -0.1362 S13: -0.0334 REMARK 3 S21: 0.1027 S22: -0.0112 S23: 0.0454 REMARK 3 S31: 0.0672 S32: -0.0525 S33: 0.0268 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 155:187) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5455 35.3953 28.8179 REMARK 3 T TENSOR REMARK 3 T11: 0.0958 T22: 0.1128 REMARK 3 T33: 0.1538 T12: -0.0057 REMARK 3 T13: -0.0106 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 4.1405 L22: 0.7644 REMARK 3 L33: 3.0557 L12: 0.0560 REMARK 3 L13: -2.4112 L23: 1.0792 REMARK 3 S TENSOR REMARK 3 S11: 0.0532 S12: -0.3529 S13: 0.1452 REMARK 3 S21: 0.0105 S22: 0.0326 S23: -0.1100 REMARK 3 S31: -0.1481 S32: 0.4089 S33: -0.0735 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 6N6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95286 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.418 REMARK 200 RESOLUTION RANGE LOW (A) : 45.806 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.72400 REMARK 200 R SYM FOR SHELL (I) : 0.72400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6N6A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE (PH 5.5) AND 15 REMARK 280 -20% POLYETHYLENE GLYCOL 3350, 25% GLYCEROL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 22.90300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.13800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.71150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.13800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.90300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.71150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 199 REMARK 465 ASN A 200 REMARK 465 GLU A 201 REMARK 465 LYS A 202 REMARK 465 THR A 203 REMARK 465 VAL A 204 REMARK 465 SER A 205 REMARK 465 MET B 1 REMARK 465 ASP B 188 REMARK 465 GLU B 189 REMARK 465 LYS B 190 REMARK 465 LYS B 191 REMARK 465 ARG B 192 REMARK 465 LYS B 193 REMARK 465 ILE B 194 REMARK 465 ILE B 195 REMARK 465 GLU B 196 REMARK 465 ASN B 197 REMARK 465 GLY B 198 REMARK 465 GLU B 199 REMARK 465 ASN B 200 REMARK 465 GLU B 201 REMARK 465 LYS B 202 REMARK 465 THR B 203 REMARK 465 VAL B 204 REMARK 465 SER B 205 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 ILE B 187 CG1 CG2 CD1 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 OH TYR B 122 O HOH B 302 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 A D 603 P A D 603 OP3 -0.119 REMARK 500 A D 603 P A D 603 OP3 -0.120 REMARK 500 A C 603 P A C 603 OP3 -0.121 REMARK 500 A C 603 P A C 603 OP3 -0.125 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 LYS A 25 -30.82 -131.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 691 DISTANCE = 5.85 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 701 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 HOH A 432 O 122.0 REMARK 620 3 HOH A 432 O 93.0 33.7 REMARK 620 4 HOH A 507 O 87.3 73.8 87.5 REMARK 620 5 HOH A 589 O 104.3 84.6 74.0 158.4 REMARK 620 6 A D 603 O3' 155.5 79.0 110.5 87.2 89.0 REMARK 620 7 A D 603 O3' 155.6 79.0 110.5 87.5 88.7 0.2 REMARK 620 8 G D 604 OP1 99.4 136.4 166.9 97.1 98.8 57.7 57.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 701 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 15 OD1 REMARK 620 2 HOH B 326 O 93.4 REMARK 620 3 HOH B 326 O 122.6 35.3 REMARK 620 4 HOH B 398 O 85.0 86.8 72.5 REMARK 620 5 HOH B 471 O 103.8 74.5 87.4 159.6 REMARK 620 6 HOH B 471 O 86.7 98.6 116.3 170.4 28.9 REMARK 620 7 A C 603 O3' 154.4 109.8 76.5 85.5 93.1 100.0 REMARK 620 8 A C 603 O3' 154.8 109.7 76.6 86.1 92.5 99.4 0.6 REMARK 620 9 G C 604 OP1 100.0 166.0 134.5 98.4 98.1 78.2 58.2 58.1 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 701 DBREF 6N6K A 1 205 UNP Q9Y3B8 ORN_HUMAN 1 205 DBREF 6N6K D 603 604 PDB 6N6K 6N6K 603 604 DBREF 6N6K B 1 205 UNP Q9Y3B8 ORN_HUMAN 1 205 DBREF 6N6K C 603 604 PDB 6N6K 6N6K 603 604 SEQRES 1 A 205 MET ALA ALA GLY GLU SER MET ALA GLN ARG MET VAL TRP SEQRES 2 A 205 VAL ASP LEU GLU MET THR GLY LEU ASP ILE GLU LYS ASP SEQRES 3 A 205 GLN ILE ILE GLU MET ALA CYS LEU ILE THR ASP SER ASP SEQRES 4 A 205 LEU ASN ILE LEU ALA GLU GLY PRO ASN LEU ILE ILE LYS SEQRES 5 A 205 GLN PRO ASP GLU LEU LEU ASP SER MET SER ASP TRP CYS SEQRES 6 A 205 LYS GLU HIS HIS GLY LYS SER GLY LEU THR LYS ALA VAL SEQRES 7 A 205 LYS GLU SER THR ILE THR LEU GLN GLN ALA GLU TYR GLU SEQRES 8 A 205 PHE LEU SER PHE VAL ARG GLN GLN THR PRO PRO GLY LEU SEQRES 9 A 205 CYS PRO LEU ALA GLY ASN SER VAL HIS GLU ASP LYS LYS SEQRES 10 A 205 PHE LEU ASP LYS TYR MET PRO GLN PHE MET LYS HIS LEU SEQRES 11 A 205 HIS TYR ARG ILE ILE ASP VAL SER THR VAL LYS GLU LEU SEQRES 12 A 205 CYS ARG ARG TRP TYR PRO GLU GLU TYR GLU PHE ALA PRO SEQRES 13 A 205 LYS LYS ALA ALA SER HIS ARG ALA LEU ASP ASP ILE SER SEQRES 14 A 205 GLU SER ILE LYS GLU LEU GLN PHE TYR ARG ASN ASN ILE SEQRES 15 A 205 PHE LYS LYS LYS ILE ASP GLU LYS LYS ARG LYS ILE ILE SEQRES 16 A 205 GLU ASN GLY GLU ASN GLU LYS THR VAL SER SEQRES 1 D 2 A G SEQRES 1 B 205 MET ALA ALA GLY GLU SER MET ALA GLN ARG MET VAL TRP SEQRES 2 B 205 VAL ASP LEU GLU MET THR GLY LEU ASP ILE GLU LYS ASP SEQRES 3 B 205 GLN ILE ILE GLU MET ALA CYS LEU ILE THR ASP SER ASP SEQRES 4 B 205 LEU ASN ILE LEU ALA GLU GLY PRO ASN LEU ILE ILE LYS SEQRES 5 B 205 GLN PRO ASP GLU LEU LEU ASP SER MET SER ASP TRP CYS SEQRES 6 B 205 LYS GLU HIS HIS GLY LYS SER GLY LEU THR LYS ALA VAL SEQRES 7 B 205 LYS GLU SER THR ILE THR LEU GLN GLN ALA GLU TYR GLU SEQRES 8 B 205 PHE LEU SER PHE VAL ARG GLN GLN THR PRO PRO GLY LEU SEQRES 9 B 205 CYS PRO LEU ALA GLY ASN SER VAL HIS GLU ASP LYS LYS SEQRES 10 B 205 PHE LEU ASP LYS TYR MET PRO GLN PHE MET LYS HIS LEU SEQRES 11 B 205 HIS TYR ARG ILE ILE ASP VAL SER THR VAL LYS GLU LEU SEQRES 12 B 205 CYS ARG ARG TRP TYR PRO GLU GLU TYR GLU PHE ALA PRO SEQRES 13 B 205 LYS LYS ALA ALA SER HIS ARG ALA LEU ASP ASP ILE SER SEQRES 14 B 205 GLU SER ILE LYS GLU LEU GLN PHE TYR ARG ASN ASN ILE SEQRES 15 B 205 PHE LYS LYS LYS ILE ASP GLU LYS LYS ARG LYS ILE ILE SEQRES 16 B 205 GLU ASN GLY GLU ASN GLU LYS THR VAL SER SEQRES 1 C 2 A G HET MLI A 301 7 HET NA D 701 1 HET NA C 701 1 HETNAM MLI MALONATE ION HETNAM NA SODIUM ION FORMUL 5 MLI C3 H2 O4 2- FORMUL 6 NA 2(NA 1+) FORMUL 8 HOH *539(H2 O) HELIX 1 AA1 GLY A 4 GLN A 9 1 6 HELIX 2 AA2 PRO A 54 SER A 60 1 7 HELIX 3 AA3 SER A 62 SER A 72 1 11 HELIX 4 AA4 GLY A 73 SER A 81 1 9 HELIX 5 AA5 THR A 84 THR A 100 1 17 HELIX 6 AA6 VAL A 112 MET A 123 1 12 HELIX 7 AA7 MET A 123 HIS A 129 1 7 HELIX 8 AA8 VAL A 137 TYR A 148 1 12 HELIX 9 AA9 TYR A 148 GLU A 153 1 6 HELIX 10 AB1 ARG A 163 PHE A 183 1 21 HELIX 11 AB2 ASP A 188 GLY A 198 1 11 HELIX 12 AB3 ALA B 3 GLN B 9 1 7 HELIX 13 AB4 PRO B 54 SER B 60 1 7 HELIX 14 AB5 SER B 62 SER B 72 1 11 HELIX 15 AB6 GLY B 73 SER B 81 1 9 HELIX 16 AB7 THR B 84 THR B 100 1 17 HELIX 17 AB8 VAL B 112 MET B 123 1 12 HELIX 18 AB9 MET B 123 HIS B 129 1 7 HELIX 19 AC1 VAL B 137 TYR B 148 1 12 HELIX 20 AC2 TYR B 148 GLU B 153 1 6 HELIX 21 AC3 ARG B 163 PHE B 183 1 21 SHEET 1 AA1 5 ILE A 42 ILE A 50 0 SHEET 2 AA1 5 ILE A 28 THR A 36 -1 N ILE A 35 O LEU A 43 SHEET 3 AA1 5 MET A 11 MET A 18 -1 N GLU A 17 O ILE A 29 SHEET 4 AA1 5 LEU A 107 GLY A 109 1 O ALA A 108 N VAL A 14 SHEET 5 AA1 5 ILE A 134 ASP A 136 1 O ILE A 135 N LEU A 107 SHEET 1 AA2 5 ILE B 42 ILE B 50 0 SHEET 2 AA2 5 ILE B 28 THR B 36 -1 N ILE B 35 O ALA B 44 SHEET 3 AA2 5 MET B 11 MET B 18 -1 N TRP B 13 O LEU B 34 SHEET 4 AA2 5 LEU B 107 GLY B 109 1 O ALA B 108 N VAL B 12 SHEET 5 AA2 5 ILE B 134 ASP B 136 1 O ILE B 135 N LEU B 107 LINK OD1 ASP A 15 NA NA D 701 1555 1555 2.32 LINK O AHOH A 432 NA NA D 701 1555 1555 2.48 LINK O BHOH A 432 NA NA D 701 1555 1555 2.23 LINK O HOH A 507 NA NA D 701 1555 1555 2.36 LINK O HOH A 589 NA NA D 701 1555 1555 2.33 LINK O3'A A D 603 NA NA D 701 1555 1555 2.59 LINK O3'B A D 603 NA NA D 701 1555 1555 2.60 LINK OP1 G D 604 NA NA D 701 1555 1555 2.47 LINK OD1 ASP B 15 NA NA C 701 1555 1555 2.31 LINK O AHOH B 326 NA NA C 701 1555 1555 2.29 LINK O BHOH B 326 NA NA C 701 1555 1555 2.57 LINK O HOH B 398 NA NA C 701 1555 1555 2.40 LINK O AHOH B 471 NA NA C 701 1555 1555 2.37 LINK O BHOH B 471 NA NA C 701 1555 1555 2.42 LINK O3'A A C 603 NA NA C 701 1555 1555 2.52 LINK O3'B A C 603 NA NA C 701 1555 1555 2.57 LINK OP1 G C 604 NA NA C 701 1555 1555 2.47 SITE 1 AC1 5 LYS A 186 ILE A 187 ARG B 97 PRO B 102 SITE 2 AC1 5 GLU B 151 SITE 1 AC2 6 ASP A 15 HOH A 432 HOH A 507 HOH A 589 SITE 2 AC2 6 A D 603 G D 604 SITE 1 AC3 6 ASP B 15 HOH B 326 HOH B 398 HOH B 471 SITE 2 AC3 6 A C 603 G C 604 CRYST1 45.806 87.423 124.276 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 0.021831 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008047 0.00000