HEADER TRANSFERASE/DNA 14-NOV-16 5TWQ TITLE POST-CATALYTIC NICKED COMPLEX OF HUMAN POLYMERASE MU WITH NEWLY TITLE 2 INCORPORATED UTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN DNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 134-494; COMPND 5 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS FAMILY X DNA POLYMERASE, NONHOMOLOGOUS END-JOINING, DNA DOUBLE STRAND KEYWDS 2 BREAK REPAIR, RIBONUCLEOTIDE INCORPORATION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.F.MOON,J.M.PRYOR,D.A.RAMSDEN,T.A.KUNKEL,K.BEBENEK,L.C.PEDERSEN REVDAT 5 04-OCT-23 5TWQ 1 LINK REVDAT 4 04-DEC-19 5TWQ 1 SOURCE REVDAT 3 27-SEP-17 5TWQ 1 JRNL REVDAT 2 20-SEP-17 5TWQ 1 REMARK REVDAT 1 05-JUL-17 5TWQ 0 JRNL AUTH A.F.MOON,J.M.PRYOR,D.A.RAMSDEN,T.A.KUNKEL,K.BEBENEK, JRNL AUTH 2 L.C.PEDERSEN JRNL TITL STRUCTURAL ACCOMMODATION OF RIBONUCLEOTIDE INCORPORATION BY JRNL TITL 2 THE DNA REPAIR ENZYME POLYMERASE MU. JRNL REF NUCLEIC ACIDS RES. V. 45 9138 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28911097 JRNL DOI 10.1093/NAR/GKX527 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 42608 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2129 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 34.9712 - 4.4358 1.00 2923 155 0.1632 0.1799 REMARK 3 2 4.4358 - 3.5219 1.00 2777 146 0.1399 0.1714 REMARK 3 3 3.5219 - 3.0770 1.00 2770 144 0.1662 0.2081 REMARK 3 4 3.0770 - 2.7958 1.00 2737 146 0.1837 0.2279 REMARK 3 5 2.7958 - 2.5955 1.00 2717 143 0.1829 0.2057 REMARK 3 6 2.5955 - 2.4425 1.00 2732 144 0.1711 0.2054 REMARK 3 7 2.4425 - 2.3202 1.00 2692 142 0.1626 0.1984 REMARK 3 8 2.3202 - 2.2192 1.00 2697 143 0.1592 0.2101 REMARK 3 9 2.2192 - 2.1338 1.00 2696 143 0.1600 0.2200 REMARK 3 10 2.1338 - 2.0602 1.00 2719 143 0.1718 0.1921 REMARK 3 11 2.0602 - 1.9958 1.00 2690 138 0.1688 0.2585 REMARK 3 12 1.9958 - 1.9387 1.00 2670 141 0.1795 0.2042 REMARK 3 13 1.9387 - 1.8877 0.99 2702 143 0.1862 0.2607 REMARK 3 14 1.8877 - 1.8416 0.96 2578 137 0.2047 0.2365 REMARK 3 15 1.8416 - 1.7998 0.88 2379 121 0.2426 0.3355 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.530 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 : 0.016 3133 REMARK 3 ANGLE : 1.416 4332 REMARK 3 CHIRALITY : 0.092 476 REMARK 3 PLANARITY : 0.009 508 REMARK 3 DIHEDRAL : 10.449 1643 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): 12.8531 -18.8508 -14.3482 REMARK 3 T TENSOR REMARK 3 T11: 0.1482 T22: 0.1453 REMARK 3 T33: 0.1262 T12: 0.0367 REMARK 3 T13: 0.0021 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 1.6503 L22: 1.1615 REMARK 3 L33: 1.5727 L12: -0.1633 REMARK 3 L13: 0.2348 L23: -0.4921 REMARK 3 S TENSOR REMARK 3 S11: 0.0467 S12: 0.2307 S13: -0.1475 REMARK 3 S21: -0.1284 S22: -0.1090 S23: -0.0932 REMARK 3 S31: 0.1644 S32: 0.2417 S33: 0.0020 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 17.2042 8.1259 -16.6204 REMARK 3 T TENSOR REMARK 3 T11: 0.2179 T22: 0.2264 REMARK 3 T33: 0.3124 T12: -0.0050 REMARK 3 T13: 0.0678 T23: 0.0649 REMARK 3 L TENSOR REMARK 3 L11: 0.6461 L22: 0.6976 REMARK 3 L33: 1.1632 L12: -0.1027 REMARK 3 L13: -0.1578 L23: 0.7551 REMARK 3 S TENSOR REMARK 3 S11: 0.1111 S12: 0.1403 S13: 0.2978 REMARK 3 S21: -0.2053 S22: -0.0075 S23: -0.2962 REMARK 3 S31: -0.2075 S32: 0.1486 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -1.8548 8.2928 -0.3208 REMARK 3 T TENSOR REMARK 3 T11: 0.1499 T22: 0.1417 REMARK 3 T33: 0.1556 T12: -0.0111 REMARK 3 T13: 0.0087 T23: -0.0292 REMARK 3 L TENSOR REMARK 3 L11: 2.1657 L22: 1.9742 REMARK 3 L33: 0.0779 L12: -0.0076 REMARK 3 L13: -0.1971 L23: -0.1293 REMARK 3 S TENSOR REMARK 3 S11: 0.0819 S12: -0.1305 S13: 0.4057 REMARK 3 S21: 0.1091 S22: -0.0671 S23: -0.1995 REMARK 3 S31: -0.0932 S32: -0.0031 S33: 0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -11.3360 -10.4150 -11.2966 REMARK 3 T TENSOR REMARK 3 T11: 0.1019 T22: 0.1132 REMARK 3 T33: 0.0900 T12: -0.0013 REMARK 3 T13: -0.0139 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 1.4665 L22: 1.3645 REMARK 3 L33: 1.8154 L12: -0.2051 REMARK 3 L13: -0.3269 L23: 0.3172 REMARK 3 S TENSOR REMARK 3 S11: 0.0542 S12: 0.2322 S13: -0.0940 REMARK 3 S21: -0.0764 S22: -0.0591 S23: 0.1794 REMARK 3 S31: 0.0240 S32: -0.2269 S33: -0.0083 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 0.2321 -6.9994 -22.4346 REMARK 3 T TENSOR REMARK 3 T11: 0.1998 T22: 0.2286 REMARK 3 T33: 0.1129 T12: 0.0057 REMARK 3 T13: -0.0062 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.9418 L22: 0.5253 REMARK 3 L33: 0.7208 L12: -0.0224 REMARK 3 L13: 0.1248 L23: -0.3023 REMARK 3 S TENSOR REMARK 3 S11: 0.0674 S12: 0.3173 S13: 0.0262 REMARK 3 S21: -0.2537 S22: -0.0122 S23: 0.0515 REMARK 3 S31: -0.0302 S32: -0.0731 S33: -0.0016 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 5TWQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000224882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42673 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.630 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: 4M04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85MM HEPES PH 7.5, 17% PEG4K, VAPOR REMARK 280 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 29.98450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.20650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.35600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.20650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.98450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.35600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 TRP A 137 REMARK 465 HIS A 365 REMARK 465 GLN A 366 REMARK 465 HIS A 367 REMARK 465 SER A 368 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 465 ALA A 384 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 GLU A 173 CD OE1 OE2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 LYS A 249 NZ REMARK 470 ARG A 256 NH1 NH2 REMARK 470 GLN A 268 CG CD OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 LEU A 280 CD1 CD2 REMARK 470 GLN A 300 OE1 NE2 REMARK 470 LYS A 339 CE NZ REMARK 470 GLN A 355 OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 465 OE1 OE2 REMARK 470 LYS A 467 CG CD CE NZ 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 -0.117 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 6 O4' - C1' - N1 ANGL. DEV. = 2.9 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 GLU A 267 9.90 -64.28 REMARK 500 GLN A 268 55.89 -156.30 REMARK 500 THR A 318 -151.68 -125.10 REMARK 500 THR A 318 -150.27 -126.92 REMARK 500 PRO A 397 104.69 -58.39 REMARK 500 SER A 411 -144.61 -163.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PPV A 505 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 A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 94.1 REMARK 620 3 VAL A 246 O 88.4 93.6 REMARK 620 4 HOH A 841 O 90.4 89.3 177.0 REMARK 620 5 DT P 3 OP1 173.3 92.5 92.5 88.4 REMARK 620 6 HOH P 114 O 83.6 176.5 88.9 88.2 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 330 OD2 47.1 REMARK 620 3 ASP A 332 OD1 92.2 113.3 REMARK 620 4 ASP A 418 OD2 139.8 93.1 100.8 REMARK 620 5 HOH A 602 O 74.3 58.3 166.5 90.6 REMARK 620 6 DA P 4 O3' 125.5 144.2 101.3 89.1 86.0 REMARK 620 7 U P 5 OP1 66.6 105.6 96.8 146.6 76.9 59.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 330 OD1 14.1 REMARK 620 3 ASP A 332 OD2 94.9 95.0 REMARK 620 4 PPV A 505 O12 168.8 162.9 96.2 REMARK 620 5 HOH A 604 O 85.2 84.7 178.2 83.7 REMARK 620 6 HOH A 655 O 92.4 78.3 87.7 89.2 90.5 REMARK 620 7 U P 5 OP1 80.0 94.1 93.0 98.2 88.7 172.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TWS RELATED DB: PDB REMARK 900 RELATED ID: 5TWR RELATED DB: PDB REMARK 900 RELATED ID: 5TWP RELATED DB: PDB DBREF 5TWQ A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 5TWQ T 1 9 PDB 5TWQ 5TWQ 1 9 DBREF 5TWQ P 1 5 PDB 5TWQ 5TWQ 1 5 DBREF 5TWQ D 1 4 PDB 5TWQ 5TWQ 1 4 SEQADV 5TWQ GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWQ SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWQ ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWQ ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWQ ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWQ A UNP Q9NP87 PRO 398 DELETION SEQADV 5TWQ A UNP Q9NP87 GLY 399 DELETION SEQADV 5TWQ A UNP Q9NP87 ALA 400 DELETION SEQADV 5TWQ A UNP Q9NP87 ALA 401 DELETION SEQADV 5TWQ A UNP Q9NP87 VAL 402 DELETION SEQADV 5TWQ A UNP Q9NP87 GLY 403 DELETION SEQADV 5TWQ A UNP Q9NP87 GLY 404 DELETION SEQADV 5TWQ A UNP Q9NP87 SER 405 DELETION SEQADV 5TWQ A UNP Q9NP87 THR 406 DELETION SEQADV 5TWQ A UNP Q9NP87 ARG 407 DELETION SEQADV 5TWQ A UNP Q9NP87 PRO 408 DELETION SEQADV 5TWQ A UNP Q9NP87 CYS 409 DELETION SEQADV 5TWQ GLY A 410 UNP Q9NP87 PRO 410 LINKER 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 9 DC DG DG DC DA DT DA DC DG SEQRES 1 P 5 DC DG DT DA U SEQRES 1 D 4 DG DC DC DG HET MN A 501 1 HET MG A 502 1 HET NA A 503 1 HET CL A 504 1 HET PPV A 505 6 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PPV PYROPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MN MN 2+ FORMUL 6 MG MG 2+ FORMUL 7 NA NA 1+ FORMUL 8 CL CL 1- FORMUL 9 PPV H4 O7 P2 FORMUL 10 EDO 3(C2 H6 O2) FORMUL 13 HOH *365(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 GLY A 345 GLN A 357 1 13 HELIX 16 AB7 PRO A 423 SER A 425 5 3 HELIX 17 AB8 GLN A 426 GLY A 436 1 11 HELIX 18 AB9 SER A 437 GLY A 453 1 17 HELIX 19 AC1 SER A 474 LEU A 482 1 9 HELIX 20 AC2 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 LEU A 334 N THR A 316 SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 AA2 5 ARG A 387 GLN A 396 -1 N PHE A 392 O VAL A 415 SHEET 5 AA2 5 ILE A 360 TYR A 362 -1 N LEU A 361 O ILE A 391 SHEET 1 AA3 3 TRP A 455 ASN A 457 0 SHEET 2 AA3 3 GLY A 460 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 O THR A 241 NA NA A 503 1555 1555 2.38 LINK O ILE A 243 NA NA A 503 1555 1555 2.35 LINK O VAL A 246 NA NA A 503 1555 1555 2.31 LINK OD1AASP A 330 MN MN A 501 1555 1555 2.58 LINK OD2BASP A 330 MN MN A 501 1555 1555 1.80 LINK OD1AASP A 330 MG MG A 502 1555 1555 2.04 LINK OD1BASP A 330 MG MG A 502 1555 1555 2.23 LINK OD1 ASP A 332 MN MN A 501 1555 1555 1.99 LINK OD2 ASP A 332 MG MG A 502 1555 1555 2.05 LINK OD2 ASP A 418 MN MN A 501 1555 1555 2.15 LINK MN MN A 501 O HOH A 602 1555 1555 2.72 LINK MN MN A 501 O3' DA P 4 1555 1555 2.77 LINK MN MN A 501 OP1 U P 5 1555 1555 2.30 LINK MG MG A 502 O12 PPV A 505 1555 1555 2.05 LINK MG MG A 502 O HOH A 604 1555 1555 2.33 LINK MG MG A 502 O HOH A 655 1555 1555 2.05 LINK MG MG A 502 OP1 U P 5 1555 1555 2.14 LINK NA NA A 503 O HOH A 841 1555 1555 2.49 LINK NA NA A 503 OP1 DT P 3 1555 1555 2.54 LINK NA NA A 503 O HOH P 114 1555 1555 2.40 CISPEP 1 GLY A 436 SER A 437 0 -6.86 SITE 1 AC1 7 ASP A 330 ASP A 332 ASP A 418 MG A 502 SITE 2 AC1 7 HOH A 602 DA P 4 U P 5 SITE 1 AC2 7 ASP A 330 ASP A 332 MN A 501 PPV A 505 SITE 2 AC2 7 HOH A 604 HOH A 655 U P 5 SITE 1 AC3 6 THR A 241 ILE A 243 VAL A 246 HOH A 841 SITE 2 AC3 6 DT P 3 HOH P 114 SITE 1 AC4 4 ASN A 457 SER A 458 EDO A 506 DA T 7 SITE 1 AC5 12 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC5 12 ASP A 332 MG A 502 HOH A 604 HOH A 655 SITE 3 AC5 12 HOH A 737 U P 5 HOH P 102 HOH P 112 SITE 1 AC6 8 ARG A 387 GLY A 433 TRP A 434 ARG A 445 SITE 2 AC6 8 SER A 458 CL A 504 DA P 4 U P 5 SITE 1 AC7 4 THR A 194 THR A 314 THR A 336 HOH A 727 SITE 1 AC8 5 PRO A 190 SER A 191 PRO A 192 GLN A 198 SITE 2 AC8 5 HOH A 673 CRYST1 59.969 68.712 110.413 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 0.016675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009057 0.00000