PDB Short entry for 5VZH HEADER TRANSFERASE/DNA 27-MAY-17 5VZH TITLE POST-CATALYTIC COMPLEX OF HUMAN POLYMERASE MU (W434H) MUTANT WITH TITLE 2 INCOMING UTP 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*TP*AP*CP*G)-3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-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: 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 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 15-NOV-23 5VZH 1 LINK ATOM REVDAT 4 04-OCT-23 5VZH 1 LINK REVDAT 3 04-DEC-19 5VZH 1 REMARK REVDAT 2 27-SEP-17 5VZH 1 JRNL REVDAT 1 05-JUL-17 5VZH 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. 1.95 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 32953 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1649 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 45.0537 - 4.4623 1.00 2831 150 0.1780 0.2058 REMARK 3 2 4.4623 - 3.5423 1.00 2701 141 0.1471 0.1552 REMARK 3 3 3.5423 - 3.0946 1.00 2665 143 0.1663 0.2001 REMARK 3 4 3.0946 - 2.8117 1.00 2667 137 0.1920 0.2192 REMARK 3 5 2.8117 - 2.6102 1.00 2647 141 0.1948 0.2457 REMARK 3 6 2.6102 - 2.4563 1.00 2611 138 0.1920 0.2204 REMARK 3 7 2.4563 - 2.3333 1.00 2635 138 0.1854 0.2247 REMARK 3 8 2.3333 - 2.2318 1.00 2627 139 0.1810 0.2153 REMARK 3 9 2.2318 - 2.1459 1.00 2607 138 0.1782 0.2262 REMARK 3 10 2.1459 - 2.0718 0.99 2611 134 0.1996 0.2372 REMARK 3 11 2.0718 - 2.0070 0.96 2527 136 0.2086 0.2705 REMARK 3 12 2.0070 - 1.9497 0.84 2175 114 0.2278 0.2609 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.140 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 : 0.007 3190 REMARK 3 ANGLE : 0.819 4436 REMARK 3 CHIRALITY : 0.043 488 REMARK 3 PLANARITY : 0.005 518 REMARK 3 DIHEDRAL : 12.408 1005 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): 12.9077 -18.7988 -14.5260 REMARK 3 T TENSOR REMARK 3 T11: 0.1538 T22: 0.1456 REMARK 3 T33: 0.1213 T12: 0.0505 REMARK 3 T13: -0.0033 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 1.3652 L22: 1.3780 REMARK 3 L33: 1.7738 L12: -0.4353 REMARK 3 L13: 0.2495 L23: -0.1294 REMARK 3 S TENSOR REMARK 3 S11: 0.0822 S12: 0.2364 S13: -0.1757 REMARK 3 S21: -0.1148 S22: -0.1229 S23: -0.1228 REMARK 3 S31: 0.1905 S32: 0.3077 S33: 0.0035 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0659 7.9652 -17.1260 REMARK 3 T TENSOR REMARK 3 T11: 0.2319 T22: 0.2479 REMARK 3 T33: 0.3429 T12: 0.0013 REMARK 3 T13: 0.1276 T23: 0.1073 REMARK 3 L TENSOR REMARK 3 L11: 0.3683 L22: 0.7904 REMARK 3 L33: 0.7065 L12: -0.1555 REMARK 3 L13: -0.2519 L23: 0.5569 REMARK 3 S TENSOR REMARK 3 S11: 0.2401 S12: 0.2905 S13: 0.4500 REMARK 3 S21: -0.3670 S22: -0.0146 S23: -0.4848 REMARK 3 S31: -0.3899 S32: 0.1315 S33: 0.0811 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -2.1805 8.7186 -0.5538 REMARK 3 T TENSOR REMARK 3 T11: 0.1393 T22: 0.1048 REMARK 3 T33: 0.1755 T12: -0.0138 REMARK 3 T13: 0.0340 T23: -0.0419 REMARK 3 L TENSOR REMARK 3 L11: 1.8307 L22: 1.7290 REMARK 3 L33: 0.4969 L12: -0.1001 REMARK 3 L13: -0.3990 L23: 0.3458 REMARK 3 S TENSOR REMARK 3 S11: 0.1437 S12: -0.1752 S13: 0.5447 REMARK 3 S21: 0.1271 S22: -0.0937 S23: -0.1990 REMARK 3 S31: -0.1340 S32: -0.0518 S33: -0.0242 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0254 -10.3923 -11.1875 REMARK 3 T TENSOR REMARK 3 T11: 0.0955 T22: 0.1280 REMARK 3 T33: 0.0853 T12: 0.0077 REMARK 3 T13: -0.0135 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 0.9393 L22: 1.4023 REMARK 3 L33: 1.0759 L12: 0.0709 REMARK 3 L13: -0.6687 L23: 0.3412 REMARK 3 S TENSOR REMARK 3 S11: 0.0685 S12: 0.3498 S13: -0.1841 REMARK 3 S21: -0.1099 S22: -0.0809 S23: 0.2168 REMARK 3 S31: -0.0046 S32: -0.2369 S33: -0.0207 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 0.6007 -8.8663 -23.2273 REMARK 3 T TENSOR REMARK 3 T11: 0.2186 T22: 0.2655 REMARK 3 T33: 0.0948 T12: 0.0390 REMARK 3 T13: -0.0224 T23: -0.0440 REMARK 3 L TENSOR REMARK 3 L11: 0.4854 L22: 0.4560 REMARK 3 L33: 0.3962 L12: 0.1568 REMARK 3 L13: -0.0970 L23: 0.1124 REMARK 3 S TENSOR REMARK 3 S11: 0.0358 S12: 0.3818 S13: -0.0150 REMARK 3 S21: -0.3393 S22: -0.0129 S23: 0.0702 REMARK 3 S31: -0.0410 S32: -0.0316 S33: 0.0302 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 5VZH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228192. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-17 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) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33554 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.010 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 (%): 56.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 90MM HEPES PH 7.5, 18% PEG4K, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 29.81850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.70200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.36100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.70200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.81850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.36100 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: 5850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 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 LEU A 196 CD1 CD2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLN A 214 CD OE1 NE2 REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 LYS A 238 CD CE NZ REMARK 470 GLN A 242 CG CD OE1 NE2 REMARK 470 LYS A 249 NZ REMARK 470 ARG A 256 NH1 NH2 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 LYS A 277 CD CE NZ REMARK 470 GLN A 281 OE1 NE2 REMARK 470 SER A 293 OG REMARK 470 ASP A 296 OD1 OD2 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 CG CD OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 LYS A 438 CD CE NZ 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 GLU A 485 CD OE1 OE2 REMARK 470 U P 5 O4' C3' O3' C2' O2' C1' N1 REMARK 470 U P 5 C2 O2 N3 C4 O4 C5 C6 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 OE1 GLU A 161 O HOH A 601 2.19 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 D 1 P DG D 1 OP3 -0.126 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 ASN A 153 41.23 -144.41 REMARK 500 THR A 318 -151.37 -126.64 REMARK 500 THR A 318 -158.67 -133.18 REMARK 500 PRO A 397 107.88 -53.05 REMARK 500 SER A 411 -142.69 -163.63 REMARK 500 ASN A 493 49.73 -86.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ANOMALOUS SIGNAL IS OBSERVED AT ONE POSITION IN THIS STRUCTURE--AT REMARK 600 THE METAL OCCUPYING THE HHH2 SITE (PEAK GREATER THAN 6.5 SIGMA). NO REMARK 600 KNOWN ANOMALOUS SCATTERERS WERE ADDED, SO THIS POSITION HAS BEEN REMARK 600 PUTATIVELY MODELED AS SODIUM (IN THE HHH2 SITE), WHICH IS REMARK 600 CONSISTENT WITH ITS IDENTITY IN OTHER REPORTED STRUCTURES 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 85.9 REMARK 620 3 VAL A 246 O 84.1 88.9 REMARK 620 4 DT P 3 OP1 175.5 91.0 92.5 REMARK 620 5 U P 5 OP1 83.9 168.7 95.0 99.4 REMARK 620 6 HOH P 105 O 102.7 89.1 172.7 80.5 88.3 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 OD2 REMARK 620 2 ASP A 332 OD1 95.8 REMARK 620 3 ASP A 418 OD2 92.5 100.7 REMARK 620 4 UTP A 506 O2A 84.1 89.9 169.2 REMARK 620 5 GOA A 507 OXT 175.0 89.2 87.3 95.2 REMARK 620 6 GOA A 507 O2 92.2 168.5 87.2 82.7 82.7 REMARK 620 N 1 2 3 4 5 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 332 OD2 93.1 REMARK 620 3 UTP A 506 O2A 93.5 92.2 REMARK 620 4 UTP A 506 O1B 173.3 91.1 91.6 REMARK 620 5 UTP A 506 O1G 88.8 176.4 90.7 86.7 REMARK 620 6 HOH A 656 O 81.8 87.1 175.2 93.2 90.2 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 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 CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UTP A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOA 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: 5TWP RELATED DB: PDB REMARK 900 RELATED ID: 5TWQ RELATED DB: PDB REMARK 900 RELATED ID: 5TWR RELATED DB: PDB REMARK 900 RELATED ID: 5TWS RELATED DB: PDB DBREF 5VZH A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 5VZH T 1 9 PDB 5VZH 5VZH 1 9 DBREF 5VZH P 1 5 PDB 5VZH 5VZH 1 5 DBREF 5VZH D 1 4 PDB 5VZH 5VZH 1 4 SEQADV 5VZH GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZH SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZH ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZH ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZH ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZH A UNP Q9NP87 PRO 398 DELETION SEQADV 5VZH A UNP Q9NP87 GLY 399 DELETION SEQADV 5VZH A UNP Q9NP87 ALA 400 DELETION SEQADV 5VZH A UNP Q9NP87 ALA 401 DELETION SEQADV 5VZH A UNP Q9NP87 VAL 402 DELETION SEQADV 5VZH A UNP Q9NP87 GLY 403 DELETION SEQADV 5VZH A UNP Q9NP87 GLY 404 DELETION SEQADV 5VZH A UNP Q9NP87 SER 405 DELETION SEQADV 5VZH A UNP Q9NP87 THR 406 DELETION SEQADV 5VZH A UNP Q9NP87 ARG 407 DELETION SEQADV 5VZH A UNP Q9NP87 PRO 408 DELETION SEQADV 5VZH A UNP Q9NP87 CYS 409 DELETION SEQADV 5VZH GLY A 410 UNP Q9NP87 PRO 410 LINKER SEQADV 5VZH HIS A 434 UNP Q9NP87 TRP 434 ENGINEERED MUTATION 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 HIS 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 MG A 502 1 HET NA A 503 1 HET CL A 504 1 HET CL A 505 1 HET UTP A 506 29 HET GOA A 507 5 HET EDO A 508 4 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM UTP URIDINE 5'-TRIPHOSPHATE HETNAM GOA GLYCOLIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN GOA HYDROXYACETIC ACID; HYDROXYETHANOIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 2(MG 2+) FORMUL 7 NA NA 1+ FORMUL 8 CL 2(CL 1-) FORMUL 10 UTP C9 H15 N2 O15 P3 FORMUL 11 GOA C2 H4 O3 FORMUL 12 EDO C2 H6 O2 FORMUL 13 HOH *258(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 2.28 LINK O ILE A 243 NA NA A 503 1555 1555 2.43 LINK O VAL A 246 NA NA A 503 1555 1555 2.37 LINK OD2 ASP A 330 MG MG A 501 1555 1555 1.97 LINK OD1 ASP A 330 MG MG A 502 1555 1555 2.03 LINK OD1 ASP A 332 MG MG A 501 1555 1555 1.99 LINK OD2 ASP A 332 MG MG A 502 1555 1555 2.09 LINK OD2 ASP A 418 MG MG A 501 1555 1555 2.03 LINK MG MG A 501 O2A UTP A 506 1555 1555 2.40 LINK MG MG A 501 OXT GOA A 507 1555 1555 2.08 LINK MG MG A 501 O2 GOA A 507 1555 1555 2.14 LINK MG MG A 502 O2A UTP A 506 1555 1555 2.14 LINK MG MG A 502 O1B UTP A 506 1555 1555 2.04 LINK MG MG A 502 O1G UTP A 506 1555 1555 2.11 LINK MG MG A 502 O HOH A 656 1555 1555 2.09 LINK NA NA A 503 OP1 DT P 3 1555 1555 2.29 LINK NA NA A 503 OP1 U P 5 1555 1555 2.22 LINK NA NA A 503 O HOH P 105 1555 1555 2.36 CISPEP 1 GLY A 436 SER A 437 0 -5.16 SITE 1 AC1 5 ASP A 330 ASP A 332 ASP A 418 UTP A 506 SITE 2 AC1 5 GOA A 507 SITE 1 AC2 4 ASP A 330 ASP A 332 UTP A 506 HOH A 656 SITE 1 AC3 6 THR A 241 ILE A 243 VAL A 246 DT P 3 SITE 2 AC3 6 U P 5 HOH P 105 SITE 1 AC4 4 LEU A 484 GLU A 485 HOH A 696 HOH A 776 SITE 1 AC5 4 ARG A 181 DG T 3 DC T 4 HOH T 113 SITE 1 AC6 24 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC6 24 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC6 24 GLY A 433 HIS A 434 THR A 435 GLY A 436 SITE 4 AC6 24 MG A 501 MG A 502 GOA A 507 HOH A 604 SITE 5 AC6 24 HOH A 639 HOH A 656 HOH A 710 HOH A 714 SITE 6 AC6 24 HOH A 716 HOH A 749 DA P 4 DA T 5 SITE 1 AC7 9 HIS A 329 ASP A 330 ASP A 332 ASP A 418 SITE 2 AC7 9 MG A 501 UTP A 506 HOH A 703 DT P 3 SITE 3 AC7 9 DA P 4 SITE 1 AC8 3 PRO A 190 SER A 191 GLN A 198 CRYST1 59.637 68.722 109.404 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 0.016768 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009140 0.00000