PDB Short entry for 5ULW HEADER THANSFERASE/DNA 25-JAN-17 5ULW TITLE STRUCTURE OF HUMAN DNA POLYMERASE IOTA BOUND TO TEMPLATE 1-METHYL- TITLE 2 DEOXYADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3'); COMPND 7 CHAIN: T; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE IOTA; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: ETA2,RAD30 HOMOLOG B; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 4 ORGANISM_TAXID: 32644; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 8 ORGANISM_TAXID: 32644; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: POLI, RAD30B; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN DNA POLYMERASE IOTA N1-METHYL-DEOXYADENOSINE DTTP TLS, KEYWDS 2 THANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.JAIN,A.K.AGGARWAL REVDAT 4 04-OCT-23 5ULW 1 REMARK REVDAT 3 18-DEC-19 5ULW 1 REMARK REVDAT 2 20-SEP-17 5ULW 1 REMARK REVDAT 1 19-APR-17 5ULW 0 JRNL AUTH R.JAIN,J.R.CHOUDHURY,A.BUKU,R.E.JOHNSON,L.PRAKASH,S.PRAKASH, JRNL AUTH 2 A.K.AGGARWAL JRNL TITL MECHANISM OF ERROR-FREE DNA SYNTHESIS ACROSS JRNL TITL 2 N1-METHYL-DEOXYADENOSINE BY HUMAN DNA POLYMERASE-IOTA. JRNL REF SCI REP V. 7 43904 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28272441 JRNL DOI 10.1038/SREP43904 REMARK 2 REMARK 2 RESOLUTION. 2.62 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) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18014 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1419 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 48.9675 - 5.6360 1.00 1828 162 0.2061 0.2294 REMARK 3 2 5.6360 - 4.4744 1.00 1703 139 0.1909 0.2012 REMARK 3 3 4.4744 - 3.9091 1.00 1659 161 0.1797 0.2327 REMARK 3 4 3.9091 - 3.5518 1.00 1660 143 0.1892 0.2491 REMARK 3 5 3.5518 - 3.2973 1.00 1638 146 0.2007 0.2539 REMARK 3 6 3.2973 - 3.1029 1.00 1630 147 0.2255 0.2941 REMARK 3 7 3.1029 - 2.9475 1.00 1637 125 0.2344 0.3602 REMARK 3 8 2.9475 - 2.8192 1.00 1635 130 0.2410 0.2673 REMARK 3 9 2.8192 - 2.7107 1.00 1599 144 0.2396 0.3045 REMARK 3 10 2.7107 - 2.6172 0.99 1606 122 0.2298 0.3039 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.810 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 : 0.008 3219 REMARK 3 ANGLE : 1.008 4431 REMARK 3 CHIRALITY : 0.051 533 REMARK 3 PLANARITY : 0.005 511 REMARK 3 DIHEDRAL : 17.753 1897 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5ULW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 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 : 14.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 2FLL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES, PH 6.0, 18 % PEG 5KMME, 0.4 REMARK 280 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 134.98200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.49100 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.23650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.74550 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 168.72750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 134.98200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 67.49100 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 33.74550 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 101.23650 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 168.72750 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, A 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 DT T 837 REMARK 465 DC T 838 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 ASP A 5 REMARK 465 VAL A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLN A 13 REMARK 465 GLY A 14 REMARK 465 VAL A 15 REMARK 465 HIS A 16 REMARK 465 ASP A 17 REMARK 465 GLN A 18 REMARK 465 VAL A 19 REMARK 465 LEU A 20 REMARK 465 PRO A 21 REMARK 465 THR A 22 REMARK 465 PRO A 23 REMARK 465 ASN A 24 REMARK 465 ALA A 25 REMARK 465 SER A 351 REMARK 465 GLU A 352 REMARK 465 LYS A 353 REMARK 465 HIS A 354 REMARK 465 TYR A 355 REMARK 465 LEU A 372 REMARK 465 GLY A 373 REMARK 465 THR A 374 REMARK 465 GLY A 375 REMARK 465 ASN A 376 REMARK 465 TYR A 377 REMARK 465 LYS A 398 REMARK 465 MET A 399 REMARK 465 PRO A 400 REMARK 465 PHE A 401 REMARK 465 HIS A 402 REMARK 465 ALA A 415 REMARK 465 LEU A 416 REMARK 465 ASN A 417 REMARK 465 THR A 418 REMARK 465 ALA A 419 REMARK 465 LYS A 420 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 DT T 839 P OP1 OP2 REMARK 470 SER A 26 OG REMARK 470 GLU A 49 CG CD OE1 OE2 REMARK 470 LYS A 51 CD CE NZ REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 TYR A 61 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 69 CD OE1 OE2 REMARK 470 LEU A 73 CD1 CD2 REMARK 470 LYS A 76 CE NZ REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 85 CD CE NZ REMARK 470 GLU A 86 CG CD OE1 OE2 REMARK 470 LYS A 87 NZ REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 GLU A 137 CD OE1 OE2 REMARK 470 LYS A 138 CD CE NZ REMARK 470 GLN A 141 CD OE1 NE2 REMARK 470 GLN A 142 CG CD OE1 NE2 REMARK 470 GLN A 144 CG CD OE1 NE2 REMARK 470 SER A 145 OG REMARK 470 ASP A 146 CG OD1 OD2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 267 CE NZ REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 VAL A 315 CG1 CG2 REMARK 470 GLU A 316 CG CD OE1 OE2 REMARK 470 LYS A 318 CG CD CE NZ REMARK 470 ASN A 319 CG OD1 ND2 REMARK 470 LYS A 320 CG CD CE NZ REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 GLU A 323 CG CD OE1 OE2 REMARK 470 ASN A 330 CG OD1 ND2 REMARK 470 GLN A 334 CG CD OE1 NE2 REMARK 470 LYS A 338 CG CD CE NZ REMARK 470 LEU A 344 CG CD1 CD2 REMARK 470 ARG A 348 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 349 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 370 CG CD OE1 NE2 REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 ASP A 385 CG OD1 OD2 REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 ASN A 396 CG OD1 ND2 REMARK 470 LEU A 403 CG CD1 CD2 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 O HOH A 644 O HOH A 664 1.83 REMARK 500 ND2 ASN A 159 O HOH A 601 2.05 REMARK 500 O HOH A 672 O HOH A 680 2.05 REMARK 500 O PHE A 308 O HOH A 602 2.17 REMARK 500 O HOH A 658 O HOH A 670 2.18 REMARK 500 O HOH A 673 O HOH A 678 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O5' DA P 867 O3' DT T 847 10665 1.73 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 DT T 844 O3' DT T 844 C3' -0.045 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 CYS A 37 63.94 24.98 REMARK 500 ASP A 52 -8.95 75.74 REMARK 500 LYS A 60 -125.33 57.49 REMARK 500 SER A 276 -81.07 -60.93 REMARK 500 CYS A 311 81.38 -151.01 REMARK 500 GLN A 370 57.05 -65.06 REMARK 500 MET A 380 -70.03 -60.70 REMARK 500 LEU A 405 148.82 -172.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 OD1 REMARK 620 2 LEU A 35 O 94.4 REMARK 620 3 ASP A 126 OD2 102.0 86.1 REMARK 620 4 TTP A 501 O1A 103.7 161.5 86.8 REMARK 620 5 TTP A 501 O1B 177.5 84.8 80.3 77.2 REMARK 620 6 TTP A 501 O3G 99.8 91.1 158.1 89.1 77.8 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 TTP 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 CL A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ULX RELATED DB: PDB DBREF 5ULW P 867 873 PDB 5ULW 5ULW 867 873 DBREF 5ULW T 837 847 PDB 5ULW 5ULW 837 847 DBREF 5ULW A 1 420 UNP Q9UNA4 POLI_HUMAN 26 445 SEQRES 1 P 7 DA DG DG DA DC DC DOC SEQRES 1 T 11 DT DC DT MA7 DG DG DG DT DC DC DT SEQRES 1 A 420 MET GLU LEU ALA ASP VAL GLY ALA ALA ALA SER SER GLN SEQRES 2 A 420 GLY VAL HIS ASP GLN VAL LEU PRO THR PRO ASN ALA SER SEQRES 3 A 420 SER ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS PHE TYR SEQRES 4 A 420 ALA GLN VAL GLU MET ILE SER ASN PRO GLU LEU LYS ASP SEQRES 5 A 420 LYS PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL VAL THR SEQRES 6 A 420 CYS ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS LYS LEU SEQRES 7 A 420 MET ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO GLN LEU SEQRES 8 A 420 VAL LEU VAL ASN GLY GLU ASP LEU THR ARG TYR ARG GLU SEQRES 9 A 420 MET SER TYR LYS VAL THR GLU LEU LEU GLU GLU PHE SER SEQRES 10 A 420 PRO VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN PHE VAL SEQRES 11 A 420 ASP LEU THR GLU MET VAL GLU LYS ARG LEU GLN GLN LEU SEQRES 12 A 420 GLN SER ASP GLU LEU SER ALA VAL THR VAL SER GLY HIS SEQRES 13 A 420 VAL TYR ASN ASN GLN SER ILE ASN LEU LEU ASP VAL LEU SEQRES 14 A 420 HIS ILE ARG LEU LEU VAL GLY SER GLN ILE ALA ALA GLU SEQRES 15 A 420 MET ARG GLU ALA MET TYR ASN GLN LEU GLY LEU THR GLY SEQRES 16 A 420 CYS ALA GLY VAL ALA SER ASN LYS LEU LEU ALA LYS LEU SEQRES 17 A 420 VAL SER GLY VAL PHE LYS PRO ASN GLN GLN THR VAL LEU SEQRES 18 A 420 LEU PRO GLU SER CYS GLN HIS LEU ILE HIS SER LEU ASN SEQRES 19 A 420 HIS ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS THR ALA SEQRES 20 A 420 LYS CYS LEU GLU ALA LEU GLY ILE ASN SER VAL ARG ASP SEQRES 21 A 420 LEU GLN THR PHE SER PRO LYS ILE LEU GLU LYS GLU LEU SEQRES 22 A 420 GLY ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SER PHE SEQRES 23 A 420 GLY GLU ASP ASN SER PRO VAL ILE LEU SER GLY PRO PRO SEQRES 24 A 420 GLN SER PHE SER GLU GLU ASP SER PHE LYS LYS CYS SER SEQRES 25 A 420 SER GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU LEU LEU SEQRES 26 A 420 ALA SER LEU LEU ASN ARG VAL CYS GLN ASP GLY ARG LYS SEQRES 27 A 420 PRO HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SER SER SEQRES 28 A 420 GLU LYS HIS TYR GLY ARG GLU SER ARG GLN CYS PRO ILE SEQRES 29 A 420 PRO SER HIS VAL ILE GLN LYS LEU GLY THR GLY ASN TYR SEQRES 30 A 420 ASP VAL MET THR PRO MET VAL ASP ILE LEU MET LYS LEU SEQRES 31 A 420 PHE ARG ASN MET VAL ASN VAL LYS MET PRO PHE HIS LEU SEQRES 32 A 420 THR LEU LEU SER VAL CYS PHE CYS ASN LEU LYS ALA LEU SEQRES 33 A 420 ASN THR ALA LYS HET DOC P 873 30 HET MA7 T 840 36 HET TTP A 501 42 HET MG A 502 1 HET CL A 503 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MA7 1N-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 1 DOC C9 H14 N3 O6 P FORMUL 2 MA7 C11 H17 N5 O6 P 1+ FORMUL 4 TTP C10 H17 N2 O14 P3 FORMUL 5 MG MG 2+ FORMUL 6 CL CL 1- FORMUL 7 HOH *87(H2 O) HELIX 1 AA1 CYS A 37 ASN A 47 1 11 HELIX 2 AA2 PRO A 48 LYS A 51 5 4 HELIX 3 AA3 ASN A 67 LEU A 73 1 7 HELIX 4 AA4 VAL A 81 CYS A 88 1 8 HELIX 5 AA5 LEU A 99 SER A 117 1 19 HELIX 6 AA6 LEU A 132 GLN A 142 1 11 HELIX 7 AA7 GLN A 144 SER A 149 1 6 HELIX 8 AA8 ASN A 159 GLN A 161 5 3 HELIX 9 AA9 ASP A 167 GLY A 192 1 26 HELIX 10 AB1 ASN A 202 GLY A 211 1 10 HELIX 11 AB2 LEU A 222 GLU A 224 5 3 HELIX 12 AB3 SER A 225 SER A 232 1 8 HELIX 13 AB4 HIS A 235 ILE A 239 5 5 HELIX 14 AB5 GLY A 243 LEU A 253 1 11 HELIX 15 AB6 SER A 257 PHE A 264 1 8 HELIX 16 AB7 SER A 265 PHE A 286 1 22 HELIX 17 AB8 SER A 313 GLY A 336 1 24 HELIX 18 AB9 PRO A 365 GLN A 370 1 6 HELIX 19 AC1 VAL A 379 VAL A 395 1 17 SHEET 1 AA1 6 VAL A 120 LEU A 123 0 SHEET 2 AA1 6 GLU A 127 ASP A 131 -1 O PHE A 129 N GLU A 121 SHEET 3 AA1 6 ILE A 30 LEU A 35 -1 N VAL A 33 O ASN A 128 SHEET 4 AA1 6 GLY A 195 ALA A 200 -1 O CYS A 196 N ASP A 34 SHEET 5 AA1 6 GLN A 218 VAL A 220 1 O THR A 219 N VAL A 199 SHEET 6 AA1 6 HIS A 156 VAL A 157 1 N HIS A 156 O GLN A 218 SHEET 1 AA2 4 MET A 79 ASN A 80 0 SHEET 2 AA2 4 LEU A 62 CYS A 66 -1 N VAL A 63 O MET A 79 SHEET 3 AA2 4 LEU A 55 GLN A 59 -1 N VAL A 57 O THR A 65 SHEET 4 AA2 4 VAL A 92 ASN A 95 1 O VAL A 94 N GLN A 58 SHEET 1 AA3 4 SER A 301 SER A 307 0 SHEET 2 AA3 4 LEU A 405 LEU A 413 -1 O PHE A 410 N PHE A 302 SHEET 3 AA3 4 PRO A 339 ARG A 347 -1 N ARG A 343 O CYS A 409 SHEET 4 AA3 4 ARG A 357 PRO A 363 -1 O GLU A 358 N ILE A 346 LINK O3' DC P 872 P DOC P 873 1555 1555 1.59 LINK O3' DT T 839 P MA7 T 840 1555 1555 1.62 LINK O3' MA7 T 840 P DG T 841 1555 1555 1.59 LINK OD1 ASP A 34 MG MG A 502 1555 1555 2.01 LINK O LEU A 35 MG MG A 502 1555 1555 2.14 LINK OD2 ASP A 126 MG MG A 502 1555 1555 2.09 LINK O1A TTP A 501 MG MG A 502 1555 1555 2.42 LINK O1B TTP A 501 MG MG A 502 1555 1555 2.32 LINK O3G TTP A 501 MG MG A 502 1555 1555 2.47 CISPEP 1 LYS A 214 PRO A 215 0 -3.41 SITE 1 AC1 20 ASP A 34 LEU A 35 ASP A 36 CYS A 37 SITE 2 AC1 20 PHE A 38 TYR A 39 VAL A 64 THR A 65 SITE 3 AC1 20 TYR A 68 ARG A 71 LYS A 77 ASP A 126 SITE 4 AC1 20 LYS A 214 MG A 502 HOH A 612 HOH A 627 SITE 5 AC1 20 HOH A 637 DOC P 873 MA7 T 840 DG T 841 SITE 1 AC2 4 ASP A 34 LEU A 35 ASP A 126 TTP A 501 SITE 1 AC3 1 ASN A 290 CRYST1 97.918 97.918 202.473 90.00 90.00 120.00 P 65 2 2 12 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 0.010213 0.005896 0.000000 0.00000 SCALE2 0.000000 0.011793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004939 0.00000