HEADER REPLICATION 03-JAN-20 6VFC TITLE DNA POLYMERASE MU, 8-OXORGTP:CT PRODUCT STATE TERNARY COMPLEX, 50 MM TITLE 2 MN2+ (2160 MIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 5 EC: 2.7.7.7; 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 (5'-D(*CP*GP*TP*AP*(8GM))-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_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLM, POLMU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630 KEYWDS TIME-LAPSE CRYSTALLOGRAPHY, OXIDIZED RIBONUCLEOTIDE INSERTION, DNA KEYWDS 2 POLYMERASE MU, DOUBLE STRAND BREAK REPAIR, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMSEN,S.H.WILSON REVDAT 2 11-OCT-23 6VFC 1 REMARK REVDAT 1 01-SEP-21 6VFC 0 JRNL AUTH J.A.JAMSEN,A.SASSA,D.D.SHOCK,W.A.BEARD,S.H.WILSON JRNL TITL DNA POLYMERASE MU, 8-OXORGTP:CT PRODUCT STATE TERNARY JRNL TITL 2 COMPLEX, 50 MM MN2+ (2160 MIN) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 58828 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2950 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 33.5490 - 4.3814 0.98 2935 160 0.1789 0.1835 REMARK 3 2 4.3814 - 3.4788 0.84 2397 120 0.1424 0.1783 REMARK 3 3 3.4788 - 3.0394 1.00 2834 145 0.1698 0.1833 REMARK 3 4 3.0394 - 2.7616 1.00 2793 163 0.1764 0.1738 REMARK 3 5 2.7616 - 2.5638 1.00 2796 142 0.1670 0.2028 REMARK 3 6 2.5638 - 2.4127 0.98 2729 138 0.1592 0.1745 REMARK 3 7 2.4127 - 2.2919 0.98 2723 159 0.1530 0.1962 REMARK 3 8 2.2919 - 2.1921 0.73 2014 109 0.1788 0.1955 REMARK 3 9 2.1921 - 2.1078 0.99 2719 144 0.1636 0.1790 REMARK 3 10 2.1078 - 2.0350 0.99 2781 132 0.1694 0.1794 REMARK 3 11 2.0350 - 1.9714 0.99 2700 145 0.1710 0.1755 REMARK 3 12 1.9714 - 1.9151 0.97 2703 139 0.1964 0.2207 REMARK 3 13 1.9151 - 1.8646 0.85 2345 111 0.2114 0.2747 REMARK 3 14 1.8646 - 1.8192 0.98 2722 151 0.1782 0.2056 REMARK 3 15 1.8192 - 1.7778 0.99 2687 153 0.1841 0.2182 REMARK 3 16 1.7778 - 1.7400 0.97 2701 133 0.1983 0.2400 REMARK 3 17 1.7400 - 1.7052 0.98 2675 150 0.2022 0.2523 REMARK 3 18 1.7052 - 1.6730 0.98 2681 137 0.2109 0.2155 REMARK 3 19 1.6730 - 1.6431 0.97 2648 150 0.2212 0.2831 REMARK 3 20 1.6431 - 1.6153 0.97 2674 130 0.2283 0.2100 REMARK 3 21 1.6153 - 1.5900 0.96 2621 139 0.2490 0.2774 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.24 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 137 THROUGH 494) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2074 -4.2749 -11.6084 REMARK 3 T TENSOR REMARK 3 T11: 0.1390 T22: 0.1502 REMARK 3 T33: 0.1306 T12: 0.0085 REMARK 3 T13: -0.0229 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.0094 L22: 1.1033 REMARK 3 L33: 0.9086 L12: -0.0687 REMARK 3 L13: -0.1841 L23: 0.4256 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: 0.0098 S13: -0.0389 REMARK 3 S21: 0.0460 S22: -0.0192 S23: -0.0440 REMARK 3 S31: -0.0012 S32: 0.0454 S33: -0.0005 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 1 THROUGH 9) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6597 -8.0930 -27.9061 REMARK 3 T TENSOR REMARK 3 T11: 0.3167 T22: 0.2329 REMARK 3 T33: 0.1886 T12: 0.0250 REMARK 3 T13: -0.0398 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.0897 L22: 0.1621 REMARK 3 L33: 0.1553 L12: 0.0799 REMARK 3 L13: -0.0314 L23: -0.1439 REMARK 3 S TENSOR REMARK 3 S11: 0.1680 S12: 0.0292 S13: 0.0258 REMARK 3 S21: -0.4932 S22: -0.1303 S23: 0.1380 REMARK 3 S31: -0.2882 S32: -0.1091 S33: 0.0017 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'P' AND RESID 1 THROUGH 5) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8566 2.4489 -17.4166 REMARK 3 T TENSOR REMARK 3 T11: 0.2941 T22: 0.2671 REMARK 3 T33: 0.2155 T12: -0.0458 REMARK 3 T13: -0.0171 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 0.0650 L22: 0.0558 REMARK 3 L33: 0.0207 L12: 0.0181 REMARK 3 L13: -0.0018 L23: 0.0273 REMARK 3 S TENSOR REMARK 3 S11: 0.2631 S12: -0.0998 S13: -0.1606 REMARK 3 S21: 0.0772 S22: -0.1647 S23: 0.2559 REMARK 3 S31: 0.1590 S32: -0.1162 S33: 0.0004 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 4) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5383 -20.1401 -29.5788 REMARK 3 T TENSOR REMARK 3 T11: 0.2615 T22: 0.2551 REMARK 3 T33: 0.2126 T12: 0.0055 REMARK 3 T13: -0.0115 T23: -0.0508 REMARK 3 L TENSOR REMARK 3 L11: 0.3144 L22: 0.3283 REMARK 3 L33: 0.5804 L12: -0.3207 REMARK 3 L13: 0.4268 L23: -0.4367 REMARK 3 S TENSOR REMARK 3 S11: 0.0120 S12: -0.1199 S13: -0.1218 REMARK 3 S21: -0.1619 S22: 0.1908 S23: 0.0371 REMARK 3 S31: 0.2455 S32: -0.2229 S33: 0.0384 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 6VFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000244066. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-19 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) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58898 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.589 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.95200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4M04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85-90MM HEPES PH 7.5, 17-18% PEG4000, REMARK 280 VAPOR DIFFUSION, SITTING 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 30.16650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.66800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.66800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.16650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.22000 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: 6960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 131 REMARK 465 PRO A 132 REMARK 465 LEU A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 ALA A 136 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 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 173 OE1 OE2 REMARK 470 GLN A 200 OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 ARG A 211 CD NE CZ NH1 NH2 REMARK 470 GLN A 214 OE1 NE2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 ARG A 230 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 249 NZ REMARK 470 GLU A 267 OE1 OE2 REMARK 470 GLN A 268 OE1 NE2 REMARK 470 GLN A 270 CB CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 274 CD OE1 NE2 REMARK 470 LYS A 277 CE NZ REMARK 470 GLN A 284 OE1 NE2 REMARK 470 GLN A 300 CG CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 GLN A 308 OE1 NE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 ASP A 356 OD1 OD2 REMARK 470 GLN A 357 CD OE1 NE2 REMARK 470 GLN A 364 CD OE1 NE2 REMARK 470 GLU A 465 OE1 OE2 REMARK 470 GLN A 466 CD OE1 NE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLN A 471 OE1 NE2 REMARK 470 GLU A 485 CD OE1 OE2 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 OD2 ASP A 330 O HOH A 601 1.81 REMARK 500 OD2 ASP A 330 O HOH A 602 2.04 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 DG T 2 O3' DG T 2 C3' -0.063 REMARK 500 DG T 3 O3' DG T 3 C3' -0.045 REMARK 500 DT T 6 P DT T 6 O5' -0.075 REMARK 500 DT P 3 O3' DT P 3 C3' -0.078 REMARK 500 DG D 1 P DG D 1 OP3 -0.124 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 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT T 6 N3 - C4 - O4 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 310 101.62 -160.45 REMARK 500 THR A 318 -153.75 -124.99 REMARK 500 THR A 318 -162.09 -129.27 REMARK 500 ASP A 330 153.63 175.62 REMARK 500 SER A 411 -151.05 -165.62 REMARK 500 SER A 437 170.05 -59.20 REMARK 500 ASN A 493 48.05 -91.62 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 EPE A 509 REMARK 610 EDO A 511 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 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 152 NE2 REMARK 620 2 HOH A 797 O 88.0 REMARK 620 3 HOH A 798 O 89.0 130.8 REMARK 620 4 HOH A 834 O 168.3 103.5 82.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 503 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 208 ND1 REMARK 620 2 DG D 1 OP3 76.2 REMARK 620 3 HOH D 209 O 82.5 85.3 REMARK 620 4 HOH D 217 O 109.8 97.1 167.6 REMARK 620 5 HOH D 218 O 170.6 98.9 89.1 78.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 504 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 219 NE2 REMARK 620 2 HOH A 603 O 71.8 REMARK 620 3 HOH A 737 O 85.0 115.6 REMARK 620 4 HOH A 826 O 143.8 93.6 71.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 506 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 86.3 91.9 REMARK 620 4 HOH A 806 O 90.1 87.7 176.4 REMARK 620 5 DT P 3 OP1 175.9 89.9 92.7 90.9 REMARK 620 6 HOH P 213 O 91.8 173.6 86.0 94.7 84.1 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 OD1 23.7 REMARK 620 3 ASP A 332 OD2 101.8 92.2 REMARK 620 4 PO4 A 507 O3 160.3 170.1 92.7 REMARK 620 5 HOH A 602 O 83.9 90.6 171.3 83.3 REMARK 620 6 HOH A 620 O 78.3 99.5 87.8 89.3 99.8 REMARK 620 7 8GM P 5 OP1 88.7 65.9 82.6 106.3 91.1 162.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN P 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 330 OD2 41.8 REMARK 620 3 ASP A 332 OD1 83.3 115.3 REMARK 620 4 ASP A 418 OD2 154.7 119.4 96.4 REMARK 620 5 HOH A 601 O 84.7 53.1 167.8 93.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 505 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 386 OE1 REMARK 620 2 GLU A 386 OE2 53.8 REMARK 620 3 HIS A 459 NE2 151.8 99.1 REMARK 620 4 HOH A 757 O 85.7 90.4 87.1 REMARK 620 5 HOH A 802 O 108.8 162.4 97.6 84.8 REMARK 620 6 HOH T 204 O 90.3 92.9 99.6 171.9 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN T 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 2 N7 REMARK 620 2 DG T 2 N7 5.4 REMARK 620 3 HOH T 201 O 95.0 93.4 REMARK 620 4 HOH T 211 O 96.5 91.6 96.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 1 N7 REMARK 620 2 HOH D 210 O 98.8 REMARK 620 3 HOH D 216 O 100.3 156.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VEZ RELATED DB: PDB DBREF 6VFC A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 6VFC T 1 9 PDB 6VFC 6VFC 1 9 DBREF 6VFC P 1 5 PDB 6VFC 6VFC 1 5 DBREF 6VFC D 1 4 PDB 6VFC 6VFC 1 4 SEQADV 6VFC GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 6VFC SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 6VFC ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6VFC ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6VFC ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6VFC A UNP Q9NP87 PRO 398 DELETION SEQADV 6VFC A UNP Q9NP87 GLY 399 DELETION SEQADV 6VFC A UNP Q9NP87 ALA 400 DELETION SEQADV 6VFC A UNP Q9NP87 ALA 401 DELETION SEQADV 6VFC A UNP Q9NP87 VAL 402 DELETION SEQADV 6VFC A UNP Q9NP87 GLY 403 DELETION SEQADV 6VFC A UNP Q9NP87 GLY 404 DELETION SEQADV 6VFC A UNP Q9NP87 SER 405 DELETION SEQADV 6VFC A UNP Q9NP87 THR 406 DELETION SEQADV 6VFC A UNP Q9NP87 ARG 407 DELETION SEQADV 6VFC A UNP Q9NP87 PRO 408 DELETION SEQADV 6VFC A UNP Q9NP87 CYS 409 DELETION SEQADV 6VFC GLY A 410 UNP Q9NP87 PRO 410 CONFLICT SEQRES 1 A 356 GLY SER ALA ALA ALA PRO LEU SER PRO ALA TRP MET PRO SEQRES 2 A 356 ALA TYR ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS SEQRES 3 A 356 ASN THR GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU SEQRES 4 A 356 ALA ALA GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR SEQRES 5 A 356 PHE CYS ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER SEQRES 6 A 356 PRO VAL THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS SEQRES 7 A 356 PHE GLY GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU SEQRES 8 A 356 GLU HIS GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SEQRES 9 A 356 SER GLU ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE SEQRES 10 A 356 PHE GLY VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG SEQRES 11 A 356 GLU GLY LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO SEQRES 12 A 356 GLN LYS LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS SEQRES 13 A 356 HIS GLN ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL SEQRES 14 A 356 ASP ALA LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN SEQRES 15 A 356 ALA LEU PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE SEQRES 16 A 356 ARG ARG GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU SEQRES 17 A 356 ILE THR HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU SEQRES 18 A 356 PRO ARG VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE SEQRES 19 A 356 LEU TYR HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO SEQRES 20 A 356 THR ARG LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU SEQRES 21 A 356 ARG SER PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER SEQRES 22 A 356 TRP LYS ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SEQRES 23 A 356 SER GLN PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER SEQRES 24 A 356 LYS LEU PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS SEQRES 25 A 356 GLU LYS GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP SEQRES 26 A 356 PRO GLU GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU SEQRES 27 A 356 ASP ILE PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO SEQRES 28 A 356 GLU GLN ARG ASN ALA SEQRES 1 T 9 DC DG DG DC DC DT DA DC DG SEQRES 1 P 5 DC DG DT DA 8GM SEQRES 1 D 4 DG DC DC DG HET 8GM P 5 24 HET MN A 501 1 HET MN A 502 1 HET MN A 503 1 HET MN A 504 1 HET MN A 505 1 HET NA A 506 1 HET PO4 A 507 5 HET DTT A 508 1 HET EPE A 509 5 HET EDO A 510 4 HET EDO A 511 3 HET EDO A 512 4 HET EDO A 513 4 HET EDO A 514 4 HET MN T 101 1 HET MN P 101 1 HET MN D 101 1 HETNAM 8GM [(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7- HETNAM 2 8GM DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 3 8GM DIHYDROGEN PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN 8GM 8-OXOGUANOSINE-5'-PHOSPHATE HETSYN DTT 1,4-DITHIOTHREITOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 3 8GM C10 H14 N5 O9 P FORMUL 5 MN 8(MN 2+) FORMUL 10 NA NA 1+ FORMUL 11 PO4 O4 P 3- FORMUL 12 DTT C4 H10 O2 S2 FORMUL 13 EPE C8 H18 N2 O4 S FORMUL 14 EDO 5(C2 H6 O2) FORMUL 22 HOH *314(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 ASP A 330 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 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 SG CYS A 180 S1 DTT A 508 1555 1555 1.91 LINK O3' DA P 4 P 8GM P 5 1555 1555 1.63 LINK NE2 HIS A 152 MN MN A 502 1555 1555 2.38 LINK ND1 HIS A 208 MN MN A 503 1555 1555 2.50 LINK NE2 HIS A 219 MN MN A 504 1555 1555 2.30 LINK O THR A 241 NA NA A 506 1555 1555 2.40 LINK O ILE A 243 NA NA A 506 1555 1555 2.43 LINK O VAL A 246 NA NA A 506 1555 1555 2.33 LINK OD1AASP A 330 MN MN A 501 1555 1555 2.16 LINK OD1BASP A 330 MN MN A 501 1555 1555 2.02 LINK OD1BASP A 330 MN MN P 101 1555 1555 2.37 LINK OD2AASP A 330 MN MN P 101 1555 1555 1.79 LINK OD2 ASP A 332 MN MN A 501 1555 1555 2.16 LINK OD1 ASP A 332 MN MN P 101 1555 1555 2.10 LINK OE1 GLU A 386 MN MN A 505 1555 1555 2.54 LINK OE2 GLU A 386 MN MN A 505 1555 1555 2.22 LINK OD2 ASP A 418 MN MN P 101 1555 1555 2.04 LINK NE2 HIS A 459 MN MN A 505 1555 1555 2.27 LINK MN MN A 501 O3 PO4 A 507 1555 1555 2.13 LINK MN MN A 501 O HOH A 602 1555 1555 2.09 LINK MN MN A 501 O HOH A 620 1555 1555 2.29 LINK MN MN A 501 OP1 8GM P 5 1555 1555 2.61 LINK MN MN A 502 O HOH A 797 1555 1555 2.21 LINK MN MN A 502 O HOH A 798 1555 1555 2.22 LINK MN MN A 502 O HOH A 834 1555 1555 2.12 LINK MN MN A 503 OP3 DG D 1 1555 1555 2.19 LINK MN MN A 503 O HOH D 209 1555 1555 2.52 LINK MN MN A 503 O HOH D 217 1555 1555 2.29 LINK MN MN A 503 O HOH D 218 1555 1555 2.39 LINK MN MN A 504 O HOH A 603 1555 1555 2.06 LINK MN MN A 504 O HOH A 737 1555 1555 1.92 LINK MN MN A 504 O HOH A 826 1555 1555 2.30 LINK MN MN A 505 O HOH A 757 1555 1555 2.26 LINK MN MN A 505 O HOH A 802 1555 1555 2.05 LINK MN MN A 505 O HOH T 204 1555 1555 2.16 LINK NA NA A 506 O HOH A 806 1555 1555 2.32 LINK NA NA A 506 OP1 DT P 3 1555 1555 2.62 LINK NA NA A 506 O HOH P 213 1555 1555 2.31 LINK O HOH A 601 MN MN P 101 1555 1555 2.18 LINK N7 A DG T 2 MN MN T 101 1555 1555 2.27 LINK N7 B DG T 2 MN MN T 101 1555 1555 2.35 LINK MN MN T 101 O HOH T 201 1555 1555 2.76 LINK MN MN T 101 O HOH T 211 1555 1555 2.43 LINK N7 DG D 1 MN MN D 101 1555 1555 2.31 LINK MN MN D 101 O HOH D 210 1555 1555 2.63 LINK MN MN D 101 O HOH D 216 1555 1555 2.24 CISPEP 1 GLY A 436 SER A 437 0 -8.25 CRYST1 60.333 62.440 119.336 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 0.016575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008380 0.00000