PDB Short entry for 4YCX HEADER TRANSFERASE/DNA 20-FEB-15 4YCX TITLE BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 2-NT GAPPED DNA TITLE 2 SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 134-494; COMPND 5 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*G)-3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 19 CHAIN: D; COMPND 20 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: POLM, POLMU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_TAXID: 9606 KEYWDS POLYMERASE, DNA REPAIR, NHEJ, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.F.MOON,R.A.GOSAVI,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK REVDAT 6 27-SEP-23 4YCX 1 LINK REVDAT 5 11-DEC-19 4YCX 1 REMARK REVDAT 4 20-SEP-17 4YCX 1 JRNL REMARK REVDAT 3 26-AUG-15 4YCX 1 JRNL REVDAT 2 19-AUG-15 4YCX 1 JRNL REVDAT 1 05-AUG-15 4YCX 0 JRNL AUTH A.F.MOON,R.A.GOSAVI,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK JRNL TITL CREATIVE TEMPLATE-DEPENDENT SYNTHESIS BY HUMAN POLYMERASE JRNL TITL 2 MU. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 E4530 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26240373 JRNL DOI 10.1073/PNAS.1505798112 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 27189 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1435 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 22.4696 - 4.5182 0.99 2880 152 0.1704 0.1933 REMARK 3 2 4.5182 - 3.5910 0.99 2754 147 0.1611 0.2012 REMARK 3 3 3.5910 - 3.1385 1.00 2725 145 0.1844 0.1936 REMARK 3 4 3.1385 - 2.8521 0.99 2685 140 0.2361 0.2710 REMARK 3 5 2.8521 - 2.6480 0.99 2708 142 0.2500 0.2936 REMARK 3 6 2.6480 - 2.4921 0.99 2702 144 0.2406 0.3179 REMARK 3 7 2.4921 - 2.3675 1.00 2686 141 0.2381 0.2603 REMARK 3 8 2.3675 - 2.2645 1.00 2684 141 0.2376 0.2638 REMARK 3 9 2.2645 - 2.1774 1.00 2685 143 0.2444 0.2916 REMARK 3 10 2.1774 - 2.1023 0.99 2680 140 0.2520 0.2987 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 3120 REMARK 3 ANGLE : 0.565 4304 REMARK 3 CHIRALITY : 0.023 472 REMARK 3 PLANARITY : 0.003 503 REMARK 3 DIHEDRAL : 11.876 996 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 137:231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8035 -18.8455 -14.2578 REMARK 3 T TENSOR REMARK 3 T11: 0.2335 T22: 0.2026 REMARK 3 T33: 0.2497 T12: 0.0454 REMARK 3 T13: -0.0039 T23: -0.0402 REMARK 3 L TENSOR REMARK 3 L11: 2.5488 L22: 1.9140 REMARK 3 L33: 3.0886 L12: -0.5610 REMARK 3 L13: -0.1595 L23: -1.0745 REMARK 3 S TENSOR REMARK 3 S11: 0.1058 S12: 0.1937 S13: -0.1347 REMARK 3 S21: -0.1492 S22: -0.1022 S23: -0.1648 REMARK 3 S31: 0.2068 S32: 0.3386 S33: 0.0047 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7675 8.4475 -17.2643 REMARK 3 T TENSOR REMARK 3 T11: 0.2820 T22: 0.2799 REMARK 3 T33: 0.2902 T12: -0.0510 REMARK 3 T13: 0.0625 T23: 0.0629 REMARK 3 L TENSOR REMARK 3 L11: 2.0479 L22: 2.4854 REMARK 3 L33: 3.5532 L12: -0.4322 REMARK 3 L13: -1.5476 L23: 1.0567 REMARK 3 S TENSOR REMARK 3 S11: 0.1979 S12: -0.0073 S13: 0.2411 REMARK 3 S21: -0.2784 S22: 0.0043 S23: -0.3551 REMARK 3 S31: -0.4218 S32: 0.3426 S33: -0.1796 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9695 8.6723 -1.1224 REMARK 3 T TENSOR REMARK 3 T11: 0.2195 T22: 0.1991 REMARK 3 T33: 0.1859 T12: 0.0087 REMARK 3 T13: 0.0226 T23: -0.0218 REMARK 3 L TENSOR REMARK 3 L11: 5.6347 L22: 3.9010 REMARK 3 L33: 0.4192 L12: 0.8340 REMARK 3 L13: -0.2433 L23: -0.2202 REMARK 3 S TENSOR REMARK 3 S11: 0.1430 S12: -0.0776 S13: 0.5833 REMARK 3 S21: 0.0495 S22: -0.1131 S23: -0.0952 REMARK 3 S31: -0.0994 S32: -0.0540 S33: -0.0253 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.8176 -10.6699 -11.3139 REMARK 3 T TENSOR REMARK 3 T11: 0.1551 T22: 0.1677 REMARK 3 T33: 0.1791 T12: -0.0257 REMARK 3 T13: -0.0045 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 2.8397 L22: 3.0540 REMARK 3 L33: 4.0434 L12: -1.1622 REMARK 3 L13: 0.1862 L23: 0.9838 REMARK 3 S TENSOR REMARK 3 S11: 0.0679 S12: 0.1930 S13: -0.0458 REMARK 3 S21: -0.1325 S22: -0.1089 S23: 0.0900 REMARK 3 S31: -0.0234 S32: -0.2357 S33: 0.0246 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID REMARK 3 1:10 ) OR ( CHAIN D AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.3315 -6.0461 -23.9365 REMARK 3 T TENSOR REMARK 3 T11: 0.2613 T22: 0.3318 REMARK 3 T33: 0.2225 T12: 0.0211 REMARK 3 T13: -0.0438 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 1.4269 L22: 4.3092 REMARK 3 L33: 1.2171 L12: 0.5097 REMARK 3 L13: -0.5229 L23: -0.3193 REMARK 3 S TENSOR REMARK 3 S11: 0.0822 S12: 0.3052 S13: 0.1037 REMARK 3 S21: -0.3853 S22: 0.0067 S23: 0.2991 REMARK 3 S31: -0.0671 S32: -0.1688 S33: -0.0532 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 4YCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207240. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28624 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.940 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: 4LZD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 20% PEG 8K, 0.2M MGCL2, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 30.02150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.41500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.34150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.41500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.02150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.34150 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, 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 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 GLY A 129 REMARK 465 SER A 130 REMARK 465 ALA A 131 REMARK 465 ALA A 132 REMARK 465 ALA A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 ALA A 136 REMARK 465 CYS A 369 REMARK 465 CYS A 370 REMARK 465 GLU A 371 REMARK 465 SER A 372 REMARK 465 PRO A 373 REMARK 465 THR A 374 REMARK 465 ARG A 375 REMARK 465 LEU A 376 REMARK 465 ALA A 377 REMARK 465 GLN A 378 REMARK 465 GLN A 379 REMARK 465 SER A 380 REMARK 465 HIS A 381 REMARK 465 MET A 382 REMARK 465 ASP A 383 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 TRP A 137 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 137 CZ3 CH2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 ARG A 211 NE CZ NH1 NH2 REMARK 470 ARG A 227 NE CZ NH1 NH2 REMARK 470 GLN A 242 CD OE1 NE2 REMARK 470 GLN A 268 CD OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 SER A 368 OG REMARK 470 GLU A 465 CG CD OE1 OE2 REMARK 470 GLN A 466 CG CD OE1 NE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLN A 471 CD OE1 NE2 REMARK 470 GLU A 485 CD OE1 OE2 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 DG D 1 P DG D 1 OP3 -0.129 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 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.5 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 HIS A 151 -152.61 -142.13 REMARK 500 THR A 318 -153.52 -123.10 REMARK 500 THR A 318 -158.24 -130.52 REMARK 500 PRO A 397 98.00 -49.01 REMARK 500 SER A 411 -145.77 -161.24 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 102.3 REMARK 620 3 ASP A 418 OD2 140.4 89.7 REMARK 620 4 HOH A 802 O 56.6 90.0 162.4 REMARK 620 5 HOH A 830 O 65.0 76.4 82.0 115.0 REMARK 620 6 HOH A 839 O 71.6 173.7 96.1 85.3 101.9 REMARK 620 7 HOH P 101 O 121.3 93.7 95.0 67.5 169.6 88.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 702 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 828 O REMARK 620 2 HOH A 977 O 98.9 REMARK 620 3 HOH A 982 O 51.2 120.5 REMARK 620 4 HOH A1027 O 114.1 76.6 156.6 REMARK 620 5 HOH P 103 O 94.2 158.3 81.2 82.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL T 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YD1 RELATED DB: PDB REMARK 900 RELATED ID: 4YD2 RELATED DB: PDB DBREF 4YCX A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 4YCX T 1 10 PDB 4YCX 4YCX 1 10 DBREF 4YCX P 1 4 PDB 4YCX 4YCX 1 4 DBREF 4YCX D 1 4 PDB 4YCX 4YCX 1 4 SEQADV 4YCX GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 4YCX SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 4YCX ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 4YCX ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 4YCX ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 4YCX A UNP Q9NP87 PRO 398 DELETION SEQADV 4YCX A UNP Q9NP87 GLY 399 DELETION SEQADV 4YCX A UNP Q9NP87 ALA 400 DELETION SEQADV 4YCX A UNP Q9NP87 ALA 401 DELETION SEQADV 4YCX A UNP Q9NP87 VAL 402 DELETION SEQADV 4YCX A UNP Q9NP87 GLY 403 DELETION SEQADV 4YCX A UNP Q9NP87 GLY 404 DELETION SEQADV 4YCX A UNP Q9NP87 SER 405 DELETION SEQADV 4YCX A UNP Q9NP87 THR 406 DELETION SEQADV 4YCX A UNP Q9NP87 ARG 407 DELETION SEQADV 4YCX A UNP Q9NP87 PRO 408 DELETION SEQADV 4YCX A UNP Q9NP87 CYS 409 DELETION SEQADV 4YCX GLY A 410 UNP Q9NP87 PRO 410 CONFLICT SEQRES 1 A 354 GLY SER ALA ALA ALA SER PRO ALA TRP MET PRO ALA TYR SEQRES 2 A 354 ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS ASN THR SEQRES 3 A 354 GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU ALA ALA SEQRES 4 A 354 GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR PHE CYS SEQRES 5 A 354 ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER PRO VAL SEQRES 6 A 354 THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS PHE GLY SEQRES 7 A 354 GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU GLU HIS SEQRES 8 A 354 GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SER GLU SEQRES 9 A 354 ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE PHE GLY SEQRES 10 A 354 VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG GLU GLY SEQRES 11 A 354 LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO GLN LYS SEQRES 12 A 354 LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS HIS GLN SEQRES 13 A 354 ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL ASP ALA SEQRES 14 A 354 LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN ALA LEU SEQRES 15 A 354 PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE ARG ARG SEQRES 16 A 354 GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU ILE THR SEQRES 17 A 354 HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU PRO ARG SEQRES 18 A 354 VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE LEU TYR SEQRES 19 A 354 HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO THR ARG SEQRES 20 A 354 LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU ARG SER SEQRES 21 A 354 PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER TRP LYS SEQRES 22 A 354 ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SER GLN SEQRES 23 A 354 PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER LYS LEU SEQRES 24 A 354 PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS GLU LYS SEQRES 25 A 354 GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP PRO GLU SEQRES 26 A 354 GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU ASP ILE SEQRES 27 A 354 PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO GLU GLN SEQRES 28 A 354 ARG ASN ALA SEQRES 1 T 10 DC DG DG DC DA DA DT DA DC DG SEQRES 1 P 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET MG A 701 1 HET NA A 702 1 HET GOL A 703 6 HET GOL A 704 6 HET IMD A 705 5 HET GOL T 101 6 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM IMD IMIDAZOLE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG MG 2+ FORMUL 6 NA NA 1+ FORMUL 7 GOL 3(C3 H8 O3) FORMUL 9 IMD C3 H5 N2 1+ FORMUL 11 HOH *291(H2 O) HELIX 1 AA1 TYR A 141 ARG A 145 5 5 HELIX 2 AA2 ASN A 153 GLU A 170 1 18 HELIX 3 AA3 SER A 172 LEU A 189 1 18 HELIX 4 AA4 THR A 195 GLN A 200 5 6 HELIX 5 AA5 GLY A 206 GLY A 220 1 15 HELIX 6 AA6 CYS A 222 SER A 231 1 10 HELIX 7 AA7 SER A 231 GLN A 242 1 12 HELIX 8 AA8 GLY A 247 GLU A 257 1 11 HELIX 9 AA9 THR A 261 GLU A 267 1 7 HELIX 10 AB1 GLN A 268 LEU A 272 5 5 HELIX 11 AB2 THR A 273 HIS A 282 1 10 HELIX 12 AB3 HIS A 282 SER A 287 1 6 HELIX 13 AB4 ARG A 292 LEU A 310 1 19 HELIX 14 AB5 THR A 318 ARG A 323 1 6 HELIX 15 AB6 LEU A 346 GLN A 357 1 12 HELIX 16 AB7 GLN A 426 GLY A 436 1 11 HELIX 17 AB8 SER A 437 GLY A 453 1 17 HELIX 18 AB9 SER A 474 LEU A 482 1 9 HELIX 19 AC1 PRO A 488 ARG A 492 5 5 SHEET 1 AA1 2 VAL A 290 LEU A 291 0 SHEET 2 AA1 2 GLN A 327 GLY A 328 -1 O GLY A 328 N VAL A 290 SHEET 1 AA2 5 THR A 314 LEU A 317 0 SHEET 2 AA2 5 VAL A 331 THR A 336 -1 O THR A 336 N THR A 314 SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 AA2 5 GLU A 386 GLN A 396 -1 N CYS A 390 O VAL A 417 SHEET 5 AA2 5 ILE A 360 GLN A 366 -1 N GLN A 366 O ARG A 387 SHEET 1 AA3 3 TRP A 455 LEU A 456 0 SHEET 2 AA3 3 LEU A 461 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK OD2 ASP A 330 MG MG A 701 1555 1555 2.31 LINK OD1 ASP A 332 MG MG A 701 1555 1555 2.18 LINK OD2 ASP A 418 MG MG A 701 1555 1555 2.11 LINK MG MG A 701 O HOH A 802 1555 1555 2.44 LINK MG MG A 701 O HOH A 830 1555 1555 2.41 LINK MG MG A 701 O HOH A 839 1555 1555 2.09 LINK MG MG A 701 O HOH P 101 1555 1555 2.07 LINK NA NA A 702 O HOH A 828 1555 1555 2.41 LINK NA NA A 702 O HOH A 977 1555 1555 2.41 LINK NA NA A 702 O HOH A 982 1555 1555 3.19 LINK NA NA A 702 O HOH A1027 1555 1555 2.41 LINK NA NA A 702 O HOH P 103 1555 1555 2.41 CISPEP 1 GLY A 436 SER A 437 0 0.44 SITE 1 AC1 7 ASP A 330 ASP A 332 ASP A 418 HOH A 802 SITE 2 AC1 7 HOH A 830 HOH A 839 HOH P 101 SITE 1 AC2 4 HOH A 828 HOH A 977 HOH A1027 HOH P 103 SITE 1 AC3 5 THR A 194 THR A 314 THR A 336 PHE A 427 SITE 2 AC3 5 HOH A 935 SITE 1 AC4 2 PHE A 469 DT T 7 SITE 1 AC5 6 GLY A 433 TRP A 434 SER A 458 HOH A 889 SITE 2 AC5 6 HOH A 892 DA P 4 SITE 1 AC6 2 DA T 6 DT T 7 CRYST1 60.043 68.683 116.830 90.00 90.00 90.00 P 21 21 21 4 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 0.016655 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008559 0.00000