PDB Short entry for 5KFY HEADER REPLICATION, TRANSFERASE/DNA 12-JUN-16 5KFY TITLE HUMAN DNA POLYMERASE ETA-DNA TERNARY COMPLEX: REACTION FIRST WITH 1 MM TITLE 2 MN2+ FOR 1800S THEN WITH 5 MM MN2+ FOR 60S AT 4 DEGREE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAD30 HOMOLOG A,XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'); COMPND 13 CHAIN: P; COMPND 14 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: POLH, RAD30, RAD30A, XPV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606 KEYWDS IN CRYSTALLO REACTION, DNA POLYMERASE, METAL ION DEPENDENT CATALYSIS, KEYWDS 2 REPLICATION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.GAO,W.YANG REVDAT 4 27-SEP-23 5KFY 1 LINK REVDAT 3 25-DEC-19 5KFY 1 REMARK REVDAT 2 20-SEP-17 5KFY 1 JRNL REMARK REVDAT 1 22-JUN-16 5KFY 0 JRNL AUTH Y.GAO,W.YANG JRNL TITL CAPTURE OF A THIRD MG2+ IS ESSENTIAL FOR CATALYZING DNA JRNL TITL 2 SYNTHESIS. JRNL REF SCIENCE V. 352 1334 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27284197 JRNL DOI 10.1126/SCIENCE.AAD9633 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 46762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.760 REMARK 3 FREE R VALUE TEST SET COUNT : 3629 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 1.7224 - 1.7001 0.00 0 136 0.0000 0.3559 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) : 23.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.83 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 : 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 5KFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222146. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-14 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 : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL-LIQUID NITROGEN REMARK 200 COOLED REMARK 200 OPTICS : 4*4 MOSIAC REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46787 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4ECQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 2000MME, 0.1 M MES, PH 6.0, REMARK 280 EVAPORATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 27.44667 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 54.89333 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 41.17000 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 68.61667 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 13.72333 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: 5750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 THR A 155 REMARK 465 THR A 156 REMARK 465 ALA A 157 REMARK 465 GLU A 158 REMARK 465 GLU A 159 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 DC T 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC T 1 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 O HOH A 921 O HOH A 956 2.11 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 O HOH A 683 O HOH T 115 6555 2.12 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 16 55.34 35.41 REMARK 500 TYR A 39 178.98 65.15 REMARK 500 LYS A 40 -38.73 -150.17 REMARK 500 SER A 62 -0.52 74.05 REMARK 500 SER A 217 -154.42 -154.13 REMARK 500 SER A 257 -7.30 90.38 REMARK 500 LYS A 428 73.02 53.67 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD1 94.5 REMARK 620 3 GLU A 116 OE2 90.6 95.4 REMARK 620 4 DTP A 505 O1A 101.4 89.1 166.8 REMARK 620 5 HOH A 829 O 86.9 168.9 95.7 79.9 REMARK 620 6 DT P 8 O3' 174.7 86.6 84.1 83.8 93.1 REMARK 620 N 1 2 3 4 5 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 ASP A 13 OD1 REMARK 620 2 MET A 14 O 84.3 REMARK 620 3 ASP A 115 OD2 102.2 85.3 REMARK 620 4 DTP A 505 O1B 165.7 90.3 90.5 REMARK 620 5 DTP A 505 O1A 103.9 168.2 84.6 83.5 REMARK 620 6 DTP A 505 O1G 84.7 101.8 170.6 83.4 87.6 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTP A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KFA RELATED DB: PDB REMARK 900 RELATED ID: 5KFB RELATED DB: PDB REMARK 900 RELATED ID: 5KFC RELATED DB: PDB REMARK 900 RELATED ID: 5KG0 RELATED DB: PDB REMARK 900 RELATED ID: 5KG1 RELATED DB: PDB REMARK 900 RELATED ID: 5KG2 RELATED DB: PDB REMARK 900 RELATED ID: 5KG3 RELATED DB: PDB REMARK 900 RELATED ID: 5KG4 RELATED DB: PDB REMARK 900 RELATED ID: 5KG5 RELATED DB: PDB REMARK 900 RELATED ID: 5KG6 RELATED DB: PDB REMARK 900 RELATED ID: 5KG7 RELATED DB: PDB REMARK 900 RELATED ID: 5KFD RELATED DB: PDB REMARK 900 RELATED ID: 5KFE RELATED DB: PDB REMARK 900 RELATED ID: 5KFS RELATED DB: PDB REMARK 900 RELATED ID: 5KFT RELATED DB: PDB REMARK 900 RELATED ID: 5KFU RELATED DB: PDB REMARK 900 RELATED ID: 5KFV RELATED DB: PDB REMARK 900 RELATED ID: 5KFW RELATED DB: PDB REMARK 900 RELATED ID: 5KFX RELATED DB: PDB REMARK 900 RELATED ID: 5KFG RELATED DB: PDB REMARK 900 RELATED ID: 5KFZ RELATED DB: PDB REMARK 900 RELATED ID: 5KFH RELATED DB: PDB REMARK 900 RELATED ID: 5KFK RELATED DB: PDB REMARK 900 RELATED ID: 5KFL RELATED DB: PDB REMARK 900 RELATED ID: 5KFI RELATED DB: PDB REMARK 900 RELATED ID: 5KFJ RELATED DB: PDB REMARK 900 RELATED ID: 5KFM RELATED DB: PDB REMARK 900 RELATED ID: 5KFN RELATED DB: PDB REMARK 900 RELATED ID: 5KFO RELATED DB: PDB REMARK 900 RELATED ID: 5KFP RELATED DB: PDB REMARK 900 RELATED ID: 5KFQ RELATED DB: PDB REMARK 900 RELATED ID: 5KFR RELATED DB: PDB REMARK 900 RELATED ID: 5KFF RELATED DB: PDB DBREF 5KFY A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 5KFY T 1 12 PDB 5KFY 5KFY 1 12 DBREF 5KFY P 1 8 PDB 5KFY 5KFY 1 8 SEQADV 5KFY GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 5KFY PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 5KFY HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQRES 1 A 435 GLY PRO HIS MET ALA THR GLY GLN ASP ARG VAL VAL ALA SEQRES 2 A 435 LEU VAL ASP MET ASP CYS PHE PHE VAL GLN VAL GLU GLN SEQRES 3 A 435 ARG GLN ASN PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL SEQRES 4 A 435 VAL GLN TYR LYS SER TRP LYS GLY GLY GLY ILE ILE ALA SEQRES 5 A 435 VAL SER TYR GLU ALA ARG ALA PHE GLY VAL THR ARG SER SEQRES 6 A 435 MET TRP ALA ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU SEQRES 7 A 435 LEU LEU ALA GLN VAL ARG GLU SER ARG GLY LYS ALA ASN SEQRES 8 A 435 LEU THR LYS TYR ARG GLU ALA SER VAL GLU VAL MET GLU SEQRES 9 A 435 ILE MET SER ARG PHE ALA VAL ILE GLU ARG ALA SER ILE SEQRES 10 A 435 ASP GLU ALA TYR VAL ASP LEU THR SER ALA VAL GLN GLU SEQRES 11 A 435 ARG LEU GLN LYS LEU GLN GLY GLN PRO ILE SER ALA ASP SEQRES 12 A 435 LEU LEU PRO SER THR TYR ILE GLU GLY LEU PRO GLN GLY SEQRES 13 A 435 PRO THR THR ALA GLU GLU THR VAL GLN LYS GLU GLY MET SEQRES 14 A 435 ARG LYS GLN GLY LEU PHE GLN TRP LEU ASP SER LEU GLN SEQRES 15 A 435 ILE ASP ASN LEU THR SER PRO ASP LEU GLN LEU THR VAL SEQRES 16 A 435 GLY ALA VAL ILE VAL GLU GLU MET ARG ALA ALA ILE GLU SEQRES 17 A 435 ARG GLU THR GLY PHE GLN CYS SER ALA GLY ILE SER HIS SEQRES 18 A 435 ASN LYS VAL LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS SEQRES 19 A 435 PRO ASN ARG GLN THR LEU VAL SER HIS GLY SER VAL PRO SEQRES 20 A 435 GLN LEU PHE SER GLN MET PRO ILE ARG LYS ILE ARG SER SEQRES 21 A 435 LEU GLY GLY LYS LEU GLY ALA SER VAL ILE GLU ILE LEU SEQRES 22 A 435 GLY ILE GLU TYR MET GLY GLU LEU THR GLN PHE THR GLU SEQRES 23 A 435 SER GLN LEU GLN SER HIS PHE GLY GLU LYS ASN GLY SER SEQRES 24 A 435 TRP LEU TYR ALA MET CYS ARG GLY ILE GLU HIS ASP PRO SEQRES 25 A 435 VAL LYS PRO ARG GLN LEU PRO LYS THR ILE GLY CYS SER SEQRES 26 A 435 LYS ASN PHE PRO GLY LYS THR ALA LEU ALA THR ARG GLU SEQRES 27 A 435 GLN VAL GLN TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU SEQRES 28 A 435 GLU GLU ARG LEU THR LYS ASP ARG ASN ASP ASN ASP ARG SEQRES 29 A 435 VAL ALA THR GLN LEU VAL VAL SER ILE ARG VAL GLN GLY SEQRES 30 A 435 ASP LYS ARG LEU SER SER LEU ARG ARG CYS CYS ALA LEU SEQRES 31 A 435 THR ARG TYR ASP ALA HIS LYS MET SER HIS ASP ALA PHE SEQRES 32 A 435 THR VAL ILE LYS ASN CYS ASN THR SER GLY ILE GLN THR SEQRES 33 A 435 GLU TRP SER PRO PRO LEU THR MET LEU PHE LEU CYS ALA SEQRES 34 A 435 THR LYS PHE SER ALA SER SEQRES 1 T 12 DC DA DT DT DA DT DG DA DC DG DC DT SEQRES 1 P 8 DA DG DC DG DT DC DA DT HET MN A 501 1 HET MN A 502 1 HET GOL A 503 6 HET GOL A 504 6 HET DTP A 505 30 HET EDO A 506 4 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 MN 2(MN 2+) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 DTP C10 H16 N5 O12 P3 FORMUL 9 EDO C2 H6 O2 FORMUL 10 HOH *439(H2 O) HELIX 1 AA1 CYS A 16 ASN A 26 1 11 HELIX 2 AA2 PRO A 27 ARG A 30 5 4 HELIX 3 AA3 SER A 51 ALA A 56 1 6 HELIX 4 AA4 TRP A 64 CYS A 72 1 9 HELIX 5 AA5 LEU A 89 SER A 104 1 16 HELIX 6 AA6 LEU A 121 GLN A 133 1 13 HELIX 7 AA7 SER A 138 LEU A 142 5 5 HELIX 8 AA8 GLN A 162 ASP A 176 1 15 HELIX 9 AA9 SER A 185 GLY A 209 1 25 HELIX 10 AB1 ASN A 219 ASN A 230 1 12 HELIX 11 AB2 SER A 239 GLY A 241 5 3 HELIX 12 AB3 SER A 242 GLN A 249 1 8 HELIX 13 AB4 MET A 250 ILE A 255 5 6 HELIX 14 AB5 GLY A 260 GLY A 271 1 12 HELIX 15 AB6 TYR A 274 PHE A 281 5 8 HELIX 16 AB7 THR A 282 GLY A 291 1 10 HELIX 17 AB8 GLY A 291 CYS A 302 1 12 HELIX 18 AB9 PRO A 326 ALA A 330 5 5 HELIX 19 AC1 ARG A 334 ASP A 360 1 27 HELIX 20 AC2 ASP A 391 LYS A 404 1 14 HELIX 21 AC3 ASN A 405 ASN A 407 5 3 SHEET 1 AA1 6 ILE A 109 SER A 113 0 SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O GLU A 116 N ALA A 112 SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119 SHEET 4 AA1 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 AA1 6 GLN A 235 LEU A 237 1 O THR A 236 N ALA A 214 SHEET 6 AA1 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 AA2 3 GLY A 46 VAL A 50 0 SHEET 2 AA2 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48 SHEET 3 AA2 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37 SHEET 1 AA3 2 GLU A 82 SER A 83 0 SHEET 2 AA3 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83 SHEET 1 AA4 3 ILE A 319 ASN A 324 0 SHEET 2 AA4 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA4 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415 SHEET 1 AA5 4 ILE A 319 ASN A 324 0 SHEET 2 AA5 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA5 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 AA5 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK OD2 ASP A 13 MN MN A 501 1555 1555 2.13 LINK OD1 ASP A 13 MN B MN A 502 1555 1555 2.20 LINK O MET A 14 MN B MN A 502 1555 1555 2.30 LINK OD1 ASP A 115 MN MN A 501 1555 1555 2.20 LINK OD2 ASP A 115 MN B MN A 502 1555 1555 2.16 LINK OE2 GLU A 116 MN MN A 501 1555 1555 2.16 LINK MN MN A 501 O1A DTP A 505 1555 1555 2.29 LINK MN MN A 501 O HOH A 829 1555 1555 2.23 LINK MN MN A 501 O3' DT P 8 1555 1555 2.35 LINK MN B MN A 502 O1B DTP A 505 1555 1555 2.18 LINK MN B MN A 502 O1A DTP A 505 1555 1555 2.32 LINK MN B MN A 502 O1G DTP A 505 1555 1555 2.24 CISPEP 1 LEU A 150 PRO A 151 0 1.24 CISPEP 2 LYS A 231 PRO A 232 0 -2.33 CISPEP 3 LYS A 231 PRO A 232 0 0.85 CISPEP 4 SER A 416 PRO A 417 0 -8.88 SITE 1 AC1 7 ASP A 13 ASP A 115 GLU A 116 MN A 502 SITE 2 AC1 7 DTP A 505 HOH A 829 DT P 8 SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 MN A 501 SITE 2 AC2 5 DTP A 505 SITE 1 AC3 8 ARG A 24 GLN A 25 PRO A 244 SER A 248 SITE 2 AC3 8 GLY A 276 HOH A 625 HOH A 653 HOH A 657 SITE 1 AC4 10 ASN A 26 PRO A 27 HIS A 28 GLY A 271 SITE 2 AC4 10 GLU A 273 TYR A 274 GLU A 277 HOH A 602 SITE 3 AC4 10 HOH A 639 HOH A 660 SITE 1 AC5 26 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC5 26 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC5 26 TYR A 52 ARG A 55 ARG A 61 ILE A 114 SITE 4 AC5 26 ASP A 115 LYS A 231 MN A 501 MN A 502 SITE 5 AC5 26 HOH A 728 HOH A 732 HOH A 758 HOH A 794 SITE 6 AC5 26 HOH A 829 HOH A 875 DT P 8 HOH P 101 SITE 7 AC5 26 DT T 4 DA T 5 SITE 1 AC6 7 ASP A 13 LYS A 224 CYS A 227 GLY A 228 SITE 2 AC6 7 LYS A 231 HOH A 646 HOH A 728 CRYST1 98.590 98.590 82.340 90.00 90.00 120.00 P 61 6 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 0.010143 0.005856 0.000000 0.00000 SCALE2 0.000000 0.011712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012145 0.00000