HEADER TRANSFERASE/DNA 14-NOV-16 5TWS TITLE POST-CATALYTIC COMPLEX OF HUMAN POLYMERASE MU (H329A) WITH NEWLY TITLE 2 INCORPORATED UTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN DNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 6 15-NOV-23 5TWS 1 LINK ATOM REVDAT 5 04-OCT-23 5TWS 1 LINK REVDAT 4 04-DEC-19 5TWS 1 SOURCE REVDAT 3 27-SEP-17 5TWS 1 JRNL REVDAT 2 20-SEP-17 5TWS 1 REMARK REVDAT 1 05-JUL-17 5TWS 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. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 39498 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1974 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 27.4810 - 4.4510 1.00 2883 150 0.1586 0.1960 REMARK 3 2 4.4510 - 3.5353 1.00 2751 146 0.1356 0.1534 REMARK 3 3 3.5353 - 3.0891 1.00 2739 145 0.1632 0.1904 REMARK 3 4 3.0891 - 2.8069 1.00 2696 141 0.1862 0.2004 REMARK 3 5 2.8069 - 2.6059 1.00 2686 138 0.1813 0.2034 REMARK 3 6 2.6059 - 2.4524 1.00 2693 146 0.1730 0.2018 REMARK 3 7 2.4524 - 2.3296 1.00 2685 141 0.1648 0.1932 REMARK 3 8 2.3296 - 2.2283 1.00 2670 137 0.1617 0.2093 REMARK 3 9 2.2283 - 2.1425 1.00 2682 142 0.1670 0.2074 REMARK 3 10 2.1425 - 2.0686 1.00 2636 143 0.1661 0.2131 REMARK 3 11 2.0686 - 2.0039 1.00 2676 138 0.1743 0.2339 REMARK 3 12 2.0039 - 1.9467 1.00 2665 144 0.1952 0.2520 REMARK 3 13 1.9467 - 1.8954 0.99 2641 134 0.2052 0.2621 REMARK 3 14 1.8954 - 1.8492 0.91 2421 129 0.2197 0.3043 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.930 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 : 0.011 3098 REMARK 3 ANGLE : 1.237 4290 REMARK 3 CHIRALITY : 0.052 477 REMARK 3 PLANARITY : 0.007 492 REMARK 3 DIHEDRAL : 12.042 976 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 138:231 REMARK 3 ORIGIN FOR THE GROUP (A): 12.8721 -18.9377 -14.3547 REMARK 3 T TENSOR REMARK 3 T11: 0.1386 T22: 0.1540 REMARK 3 T33: 0.1127 T12: 0.0486 REMARK 3 T13: -0.0060 T23: -0.0187 REMARK 3 L TENSOR REMARK 3 L11: 0.0746 L22: 0.0895 REMARK 3 L33: 0.0859 L12: -0.0643 REMARK 3 L13: 0.0012 L23: 0.0149 REMARK 3 S TENSOR REMARK 3 S11: 0.0623 S12: 0.1539 S13: -0.1423 REMARK 3 S21: -0.0320 S22: -0.0923 S23: 0.0055 REMARK 3 S31: 0.1540 S32: 0.1503 S33: -0.0361 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 17.1956 8.0724 -16.7801 REMARK 3 T TENSOR REMARK 3 T11: 0.1558 T22: 0.2026 REMARK 3 T33: 0.2858 T12: -0.0050 REMARK 3 T13: 0.1149 T23: 0.1179 REMARK 3 L TENSOR REMARK 3 L11: 0.0259 L22: 0.0297 REMARK 3 L33: 0.0677 L12: -0.0206 REMARK 3 L13: 0.0025 L23: -0.0102 REMARK 3 S TENSOR REMARK 3 S11: 0.0581 S12: 0.0993 S13: 0.2447 REMARK 3 S21: -0.0862 S22: -0.0358 S23: -0.1946 REMARK 3 S31: -0.1122 S32: 0.0674 S33: -0.0411 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -2.4235 8.5096 -0.3752 REMARK 3 T TENSOR REMARK 3 T11: 0.0811 T22: 0.0712 REMARK 3 T33: 0.1707 T12: -0.0103 REMARK 3 T13: 0.0218 T23: -0.0316 REMARK 3 L TENSOR REMARK 3 L11: 0.1417 L22: 0.1294 REMARK 3 L33: 0.0553 L12: 0.0368 REMARK 3 L13: 0.0646 L23: 0.0269 REMARK 3 S TENSOR REMARK 3 S11: 0.1120 S12: -0.1714 S13: 0.2883 REMARK 3 S21: 0.0538 S22: -0.0730 S23: -0.1229 REMARK 3 S31: -0.0099 S32: -0.0570 S33: 0.0657 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -11.1415 -10.2921 -11.4262 REMARK 3 T TENSOR REMARK 3 T11: 0.0874 T22: 0.1062 REMARK 3 T33: 0.0785 T12: 0.0004 REMARK 3 T13: -0.0126 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.0448 L22: 0.0594 REMARK 3 L33: 0.0779 L12: -0.0108 REMARK 3 L13: -0.0476 L23: 0.0026 REMARK 3 S TENSOR REMARK 3 S11: 0.0453 S12: 0.1319 S13: -0.0671 REMARK 3 S21: 0.0053 S22: -0.0399 S23: 0.0777 REMARK 3 S31: 0.0290 S32: -0.0691 S33: 0.0039 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 0.2358 -8.7587 -22.8046 REMARK 3 T TENSOR REMARK 3 T11: 0.1816 T22: 0.2248 REMARK 3 T33: 0.0634 T12: 0.0195 REMARK 3 T13: -0.0198 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 0.1944 L22: 0.0596 REMARK 3 L33: 0.0527 L12: 0.0463 REMARK 3 L13: -0.0661 L23: -0.0213 REMARK 3 S TENSOR REMARK 3 S11: 0.0692 S12: 0.3655 S13: 0.0556 REMARK 3 S21: -0.1129 S22: -0.0086 S23: 0.0350 REMARK 3 S31: 0.0117 S32: -0.0249 S33: 0.1007 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 5TWS 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_1000224940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39735 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.960 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: 62MM HEPES PH 7.5, 12.4% 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 29.96750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.15950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.42900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.15950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.96750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.42900 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: 5570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 CG CD OE1 OE2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLU A 218 CD OE1 OE2 REMARK 470 LYS A 249 CE NZ REMARK 470 GLU A 267 CG CD OE1 OE2 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 CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 465 CD OE1 OE2 REMARK 470 GLN A 466 OE1 NE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLU A 485 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 DC T 1 O3' DC T 1 C3' -0.053 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 6 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA T 7 O5' - P - OP1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC P 1 O4' - C1' - N1 ANGL. DEV. = 2.1 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 -159.71 -152.55 REMARK 500 ASN A 153 40.75 -142.07 REMARK 500 THR A 318 -153.87 -125.50 REMARK 500 THR A 318 -150.51 -129.12 REMARK 500 PRO A 397 104.55 -55.53 REMARK 500 SER A 411 -148.43 -166.00 REMARK 500 ASN A 493 49.21 -85.92 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 T 132 DISTANCE = 6.63 ANGSTROMS 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 EPE A 510 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 508 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 98.0 REMARK 620 3 VAL A 246 O 89.9 93.1 REMARK 620 4 HOH A 814 O 87.0 90.1 175.8 REMARK 620 5 DT P 3 OP1 169.2 92.5 92.6 89.9 REMARK 620 6 HOH P 118 O 83.8 178.2 87.1 89.7 85.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 95.5 REMARK 620 3 GOA A 503 O2 94.1 170.4 REMARK 620 4 GOA A 503 OXT 169.7 93.7 76.7 REMARK 620 5 HOH A 735 O 85.9 89.4 91.7 89.8 REMARK 620 6 U P 5 OP1 86.5 93.9 86.3 97.2 172.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD1 94.6 REMARK 620 3 ASP A 418 OD2 146.5 95.3 REMARK 620 4 DA P 4 O3' 126.6 97.5 83.6 REMARK 620 5 U P 5 OP1 71.4 94.0 139.4 56.0 REMARK 620 6 HOH P 107 O 80.4 171.9 92.4 80.6 78.4 REMARK 620 N 1 2 3 4 5 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOA 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 CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TWR RELATED DB: PDB REMARK 900 RELATED ID: 5TWQ RELATED DB: PDB REMARK 900 RELATED ID: 5TWP RELATED DB: PDB DBREF 5TWS A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 5TWS T 1 9 PDB 5TWS 5TWS 1 9 DBREF 5TWS P 1 5 PDB 5TWS 5TWS 1 5 DBREF 5TWS D 1 4 PDB 5TWS 5TWS 1 4 SEQADV 5TWS GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWS SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWS ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWS ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWS ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 5TWS ALA A 329 UNP Q9NP87 HIS 329 ENGINEERED MUTATION SEQADV 5TWS A UNP Q9NP87 PRO 398 DELETION SEQADV 5TWS A UNP Q9NP87 GLY 399 DELETION SEQADV 5TWS A UNP Q9NP87 ALA 400 DELETION SEQADV 5TWS A UNP Q9NP87 ALA 401 DELETION SEQADV 5TWS A UNP Q9NP87 VAL 402 DELETION SEQADV 5TWS A UNP Q9NP87 GLY 403 DELETION SEQADV 5TWS A UNP Q9NP87 GLY 404 DELETION SEQADV 5TWS A UNP Q9NP87 SER 405 DELETION SEQADV 5TWS A UNP Q9NP87 THR 406 DELETION SEQADV 5TWS A UNP Q9NP87 ARG 407 DELETION SEQADV 5TWS A UNP Q9NP87 PRO 408 DELETION SEQADV 5TWS A UNP Q9NP87 CYS 409 DELETION SEQADV 5TWS 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 ALA 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 MG A 501 1 HET NA A 502 1 HET GOA A 503 5 HET CL A 504 1 HET CL A 505 1 HET CL A 506 1 HET CL A 507 1 HET NA A 508 1 HET EDO A 509 4 HET EPE A 510 9 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM GOA GLYCOLIC ACID HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN GOA HYDROXYACETIC ACID; HYDROXYETHANOIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 5 MG MG 2+ FORMUL 6 NA 2(NA 1+) FORMUL 7 GOA C2 H4 O3 FORMUL 8 CL 4(CL 1-) FORMUL 13 EDO C2 H6 O2 FORMUL 14 EPE C8 H18 N2 O4 S FORMUL 15 HOH *328(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 ALA A 188 1 17 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 508 1555 1555 2.36 LINK O ILE A 243 NA NA A 508 1555 1555 2.30 LINK O VAL A 246 NA NA A 508 1555 1555 2.32 LINK OD1 ASP A 330 MG MG A 501 1555 1555 2.15 LINK OD1 ASP A 330 NA NA A 502 1555 1555 2.60 LINK OD2 ASP A 332 MG MG A 501 1555 1555 2.05 LINK OD1 ASP A 332 NA NA A 502 1555 1555 2.10 LINK OD2 ASP A 418 NA NA A 502 1555 1555 2.23 LINK MG MG A 501 O2 GOA A 503 1555 1555 2.22 LINK MG MG A 501 OXT GOA A 503 1555 1555 2.10 LINK MG MG A 501 O HOH A 735 1555 1555 2.11 LINK MG MG A 501 OP1 U P 5 1555 1555 2.07 LINK NA NA A 502 O3' DA P 4 1555 1555 2.87 LINK NA NA A 502 OP1 U P 5 1555 1555 2.33 LINK NA NA A 502 O HOH P 107 1555 1555 2.71 LINK NA NA A 508 O HOH A 814 1555 1555 2.50 LINK NA NA A 508 OP1 DT P 3 1555 1555 2.64 LINK NA NA A 508 O HOH P 118 1555 1555 2.51 CISPEP 1 GLY A 436 SER A 437 0 -6.02 SITE 1 AC1 6 ASP A 330 ASP A 332 NA A 502 GOA A 503 SITE 2 AC1 6 HOH A 735 U P 5 SITE 1 AC2 7 ASP A 330 ASP A 332 ASP A 418 MG A 501 SITE 2 AC2 7 DA P 4 U P 5 HOH P 107 SITE 1 AC3 11 GLY A 319 GLY A 320 ARG A 323 ASP A 330 SITE 2 AC3 11 ASP A 332 MG A 501 HOH A 652 HOH A 732 SITE 3 AC3 11 HOH A 735 U P 5 HOH P 102 SITE 1 AC4 5 ARG A 445 ASN A 457 SER A 458 EDO A 509 SITE 2 AC4 5 DA T 7 SITE 1 AC5 2 THR A 468 PHE A 469 SITE 1 AC6 3 SER A 231 GLU A 232 ARG A 233 SITE 1 AC7 2 ARG A 393 HOH A 808 SITE 1 AC8 6 THR A 241 ILE A 243 VAL A 246 HOH A 814 SITE 2 AC8 6 DT P 3 HOH P 118 SITE 1 AC9 7 ARG A 387 GLY A 433 TRP A 434 ARG A 445 SITE 2 AC9 7 CL A 504 DA P 4 U P 5 SITE 1 AD1 4 LYS A 325 LEU A 326 GLN A 327 HOH A 622 CRYST1 59.935 68.858 110.319 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 0.016685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009065 0.00000