PDB Short entry for 6X6Z HEADER REPLICATION/DNA 29-MAY-20 6X6Z TITLE REV1 TERNARY COMPLEX WITH DCTP AND CA2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*G)-3'); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*CP*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'); COMPND 8 CHAIN: T; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA REPAIR PROTEIN REV1; COMPND 12 CHAIN: A; COMPND 13 SYNONYM: REVERSIONLESS PROTEIN 1; COMPND 14 EC: 2.7.7.-; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 GENE: REV1, YOR346W, O6339; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, REPLICATION, REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.M.WEAVER,B.D.FREUDENTHAL REVDAT 3 18-OCT-23 6X6Z 1 REMARK REVDAT 2 21-OCT-20 6X6Z 1 JRNL REVDAT 1 30-SEP-20 6X6Z 0 JRNL AUTH T.M.WEAVER,L.M.CORTEZ,T.H.KHOANG,M.T.WASHINGTON,P.K.AGARWAL, JRNL AUTH 2 B.D.FREUDENTHAL JRNL TITL VISUALIZING REV1 CATALYZE PROTEIN-TEMPLATE DNA SYNTHESIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 25494 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32999062 JRNL DOI 10.1073/PNAS.2010484117 REMARK 2 REMARK 2 RESOLUTION. 1.40 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 198840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.890 REMARK 3 FREE R VALUE TEST SET COUNT : 3751 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 35.2600 - 4.2000 1.00 7498 145 0.1659 0.1871 REMARK 3 2 4.2000 - 3.3300 1.00 7491 141 0.1484 0.1506 REMARK 3 3 3.3300 - 2.9100 1.00 7508 139 0.1735 0.2017 REMARK 3 4 2.9100 - 2.6500 1.00 7504 144 0.1855 0.2186 REMARK 3 5 2.6500 - 2.4600 0.99 7424 143 0.1822 0.1897 REMARK 3 6 2.4600 - 2.3100 0.99 7373 135 0.1802 0.2047 REMARK 3 7 2.3100 - 2.2000 0.98 7374 140 0.1725 0.1960 REMARK 3 8 2.2000 - 2.1000 0.97 7319 146 0.1639 0.1952 REMARK 3 9 2.1000 - 2.0200 0.97 7329 140 0.1708 0.2023 REMARK 3 10 2.0200 - 1.9500 0.97 7253 142 0.1777 0.1989 REMARK 3 11 1.9500 - 1.8900 0.97 7308 141 0.1923 0.2076 REMARK 3 12 1.8900 - 1.8300 0.97 7330 140 0.2170 0.2562 REMARK 3 13 1.8300 - 1.7900 0.97 7287 137 0.2054 0.2726 REMARK 3 14 1.7900 - 1.7400 0.97 7324 145 0.2098 0.2736 REMARK 3 15 1.7400 - 1.7000 0.98 7331 135 0.2053 0.2296 REMARK 3 16 1.7000 - 1.6700 0.97 7302 145 0.2069 0.2266 REMARK 3 17 1.6700 - 1.6300 0.97 7290 137 0.2179 0.2595 REMARK 3 18 1.6300 - 1.6000 0.97 7284 146 0.2227 0.2264 REMARK 3 19 1.6000 - 1.5700 0.97 7290 139 0.2335 0.2657 REMARK 3 20 1.5700 - 1.5500 0.96 7251 141 0.2431 0.2405 REMARK 3 21 1.5500 - 1.5200 0.96 7150 134 0.2497 0.2900 REMARK 3 22 1.5200 - 1.5000 0.95 7159 140 0.2626 0.2512 REMARK 3 23 1.5000 - 1.4800 0.94 6994 139 0.2773 0.2827 REMARK 3 24 1.4800 - 1.4600 0.93 7004 136 0.2904 0.3226 REMARK 3 25 1.4600 - 1.4400 0.92 6872 128 0.3011 0.3271 REMARK 3 26 1.4400 - 1.4200 0.91 6838 135 0.3110 0.3063 REMARK 3 27 1.4200 - 1.4000 0.80 6002 118 0.3224 0.2970 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) : 0.164 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.451 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.41 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 4325 REMARK 3 ANGLE : 0.999 5984 REMARK 3 CHIRALITY : 0.078 667 REMARK 3 PLANARITY : 0.005 669 REMARK 3 DIHEDRAL : 19.804 1669 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 6X6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R 200K-A REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 198840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 35.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHASER REMARK 200 STARTING MODEL: 5WM1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-23% PEG3350 AND 200 MM AMMONIUM REMARK 280 NITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 31.18800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.64500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.97350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.64500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.18800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.97350 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 LYS A 305 REMARK 465 ARG A 306 REMARK 465 LEU A 745 REMARK 465 LYS A 746 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 470 TYR A 347 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR A 348 OG1 CG2 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 TYR A 347 -65.12 -104.82 REMARK 500 CYS A 365 66.47 26.51 REMARK 500 LYS A 396 -92.72 -133.02 REMARK 500 ASN A 397 51.76 -91.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1551 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1552 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1553 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A1554 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A1555 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A1556 DISTANCE = 6.54 ANGSTROMS 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 CA P 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 11 OP1 REMARK 620 2 HOH P 219 O 86.7 REMARK 620 3 ASP A 548 O 169.7 84.4 REMARK 620 4 LEU A 550 O 96.1 175.7 93.0 REMARK 620 5 VAL A 553 O 96.7 83.6 87.6 92.9 REMARK 620 6 HOH A1384 O 88.2 92.1 86.9 91.1 173.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA P 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 12 O3' REMARK 620 2 ASP A 362 OD1 179.4 REMARK 620 3 ASP A 467 OD1 85.8 93.7 REMARK 620 4 ASP A 467 OD2 111.8 67.6 43.5 REMARK 620 5 GLU A 468 OE2 91.5 89.1 117.0 144.5 REMARK 620 6 DCP A 801 O2A 92.8 87.1 105.8 70.5 137.2 REMARK 620 7 HOH A1197 O 93.5 87.1 178.0 135.5 64.9 72.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 803 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 362 OD1 REMARK 620 2 ASP A 362 OD2 52.5 REMARK 620 3 PHE A 363 O 110.6 74.1 REMARK 620 4 ASP A 467 OD2 78.7 116.1 91.3 REMARK 620 5 DCP A 801 O2A 81.4 116.6 167.8 89.0 REMARK 620 6 DCP A 801 O2B 159.2 147.2 86.8 90.1 81.0 REMARK 620 7 DCP A 801 O3G 108.9 77.3 96.6 166.1 80.8 78.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA P 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCP A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 803 DBREF 6X6Z P 1 12 PDB 6X6Z 6X6Z 1 12 DBREF 6X6Z T 1 17 PDB 6X6Z 6X6Z 1 17 DBREF 6X6Z A 305 746 UNP P12689 REV1_YEAST 305 746 SEQRES 1 P 12 DG DG DG DG DT DG DT DG DG DT DA DG SEQRES 1 T 17 DC DA DT DC DG DC DT DA DC DC DA DC DA SEQRES 2 T 17 DC DC DC DC SEQRES 1 A 442 LYS ARG ILE VAL ALA CYS ASP ASP PRO ASP PHE LEU THR SEQRES 2 A 442 SER TYR PHE ALA HIS SER ARG LEU HIS HIS LEU SER ALA SEQRES 3 A 442 TRP LYS ALA ASN LEU LYS ASP LYS PHE LEU ASN GLU ASN SEQRES 4 A 442 ILE HIS LYS TYR THR LYS ILE THR ASP LYS ASP THR TYR SEQRES 5 A 442 ILE ILE PHE HIS ILE ASP PHE ASP CYS PHE PHE ALA THR SEQRES 6 A 442 VAL ALA TYR LEU CYS ARG SER SER SER PHE SER ALA CYS SEQRES 7 A 442 ASP PHE LYS ARG ASP PRO ILE VAL VAL CYS HIS GLY THR SEQRES 8 A 442 LYS ASN SER ASP ILE ALA SER CYS ASN TYR VAL ALA ARG SEQRES 9 A 442 SER TYR GLY ILE LYS ASN GLY MET TRP VAL SER GLN ALA SEQRES 10 A 442 GLU LYS MET LEU PRO ASN GLY ILE LYS LEU ILE SER LEU SEQRES 11 A 442 PRO TYR THR PHE GLU GLN PHE GLN LEU LYS SER GLU ALA SEQRES 12 A 442 PHE TYR SER THR LEU LYS ARG LEU ASN ILE PHE ASN LEU SEQRES 13 A 442 ILE LEU PRO ILE SER ILE ASP GLU ALA VAL CYS VAL ARG SEQRES 14 A 442 ILE ILE PRO ASP ASN ILE HIS ASN THR ASN THR LEU ASN SEQRES 15 A 442 ALA ARG LEU CYS GLU GLU ILE ARG GLN GLU ILE PHE GLN SEQRES 16 A 442 GLY THR ASN GLY CYS THR VAL SER ILE GLY CYS SER ASP SEQRES 17 A 442 SER LEU VAL LEU ALA ARG LEU ALA LEU LYS MET ALA LYS SEQRES 18 A 442 PRO ASN GLY TYR ASN ILE THR PHE LYS SER ASN LEU SER SEQRES 19 A 442 GLU GLU PHE TRP SER SER PHE LYS LEU ASP ASP LEU PRO SEQRES 20 A 442 GLY VAL GLY HIS SER THR LEU SER ARG LEU GLU SER THR SEQRES 21 A 442 PHE ASP SER PRO HIS SER LEU ASN ASP LEU ARG LYS ARG SEQRES 22 A 442 TYR THR LEU ASP ALA LEU LYS ALA SER VAL GLY SER LYS SEQRES 23 A 442 LEU GLY MET LYS ILE HIS LEU ALA LEU GLN GLY GLN ASP SEQRES 24 A 442 ASP GLU GLU SER LEU LYS ILE LEU TYR ASP PRO LYS GLU SEQRES 25 A 442 VAL LEU GLN ARG LYS SER LEU SER ILE ASP ILE ASN TRP SEQRES 26 A 442 GLY ILE ARG PHE LYS ASN ILE THR GLN VAL ASP LEU PHE SEQRES 27 A 442 ILE GLU ARG GLY CYS GLN TYR LEU LEU GLU LYS LEU ASN SEQRES 28 A 442 GLU ILE ASN LYS THR THR SER GLN ILE THR LEU LYS LEU SEQRES 29 A 442 MET ARG ARG CYS LYS ASP ALA PRO ILE GLU PRO PRO LYS SEQRES 30 A 442 TYR MET GLY MET GLY ARG CYS ASP SER PHE SER ARG SER SEQRES 31 A 442 SER ARG LEU GLY ILE PRO THR ASN GLU PHE GLY ILE ILE SEQRES 32 A 442 ALA THR GLU MET LYS SER LEU TYR ARG THR LEU GLY CYS SEQRES 33 A 442 PRO PRO MET GLU LEU ARG GLY LEU ALA LEU GLN PHE ASN SEQRES 34 A 442 LYS LEU VAL ASP VAL GLY PRO ASP ASN ASN GLN LEU LYS HET CA P 101 1 HET CA P 102 1 HET DCP A 801 28 HET GOL A 802 6 HET CA A 803 1 HETNAM CA CALCIUM ION HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 CA 3(CA 2+) FORMUL 6 DCP C9 H16 N3 O13 P3 FORMUL 7 GOL C3 H8 O3 FORMUL 9 HOH *764(H2 O) HELIX 1 AA1 ASP A 314 SER A 323 1 10 HELIX 2 AA2 SER A 323 ASN A 343 1 21 HELIX 3 AA3 CYS A 365 CYS A 374 1 10 HELIX 4 AA4 SER A 376 SER A 380 5 5 HELIX 5 AA5 ASN A 404 SER A 409 1 6 HELIX 6 AA6 TRP A 417 LYS A 423 1 7 HELIX 7 AA7 THR A 437 LEU A 455 1 19 HELIX 8 AA8 THR A 482 THR A 501 1 20 HELIX 9 AA9 SER A 513 LYS A 525 1 13 HELIX 10 AB1 PHE A 533 LEU A 537 5 5 HELIX 11 AB2 SER A 538 SER A 543 1 6 HELIX 12 AB3 SER A 544 PHE A 545 5 2 HELIX 13 AB4 LYS A 546 LEU A 550 5 5 HELIX 14 AB5 GLY A 554 PHE A 565 1 12 HELIX 15 AB6 SER A 570 TYR A 578 1 9 HELIX 16 AB7 THR A 579 GLY A 588 1 10 HELIX 17 AB8 GLY A 588 LEU A 599 1 12 HELIX 18 AB9 ASP A 604 ASP A 613 1 10 HELIX 19 AC1 ASP A 613 GLN A 619 1 7 HELIX 20 AC2 ASN A 635 ILE A 657 1 23 HELIX 21 AC3 GLU A 703 GLY A 719 1 17 HELIX 22 AC4 PRO A 721 MET A 723 5 3 SHEET 1 AA1 5 LEU A 460 SER A 465 0 SHEET 2 AA1 5 GLU A 468 ILE A 474 -1 O VAL A 472 N LEU A 460 SHEET 3 AA1 5 TYR A 356 PHE A 363 -1 N PHE A 359 O CYS A 471 SHEET 4 AA1 5 VAL A 506 SER A 511 -1 O SER A 511 N ILE A 358 SHEET 5 AA1 5 TYR A 529 ILE A 531 1 O ASN A 530 N CYS A 510 SHEET 1 AA2 3 SER A 402 CYS A 403 0 SHEET 2 AA2 3 ILE A 389 VAL A 391 -1 N VAL A 391 O SER A 402 SHEET 3 AA2 3 ILE A 432 LEU A 434 1 O LEU A 434 N VAL A 390 SHEET 1 AA3 4 LEU A 623 ILE A 627 0 SHEET 2 AA3 4 LEU A 725 ASP A 737 -1 O PHE A 732 N LEU A 623 SHEET 3 AA3 4 LYS A 659 ARG A 671 -1 N MET A 669 O ARG A 726 SHEET 4 AA3 4 CYS A 688 THR A 701 -1 O ASP A 689 N ARG A 670 LINK OP1 DA P 11 CA CA P 102 1555 1555 2.57 LINK O3' DG P 12 CA CA P 101 1555 1555 2.54 LINK CA CA P 101 OD1 ASP A 362 1555 1555 2.34 LINK CA CA P 101 OD1 ASP A 467 1555 1555 2.41 LINK CA CA P 101 OD2 ASP A 467 1555 1555 3.19 LINK CA CA P 101 OE2 GLU A 468 1555 1555 2.22 LINK CA CA P 101 O2A DCP A 801 1555 1555 2.37 LINK CA CA P 101 O HOH A1197 1555 1555 2.97 LINK CA CA P 102 O HOH P 219 1555 1555 2.53 LINK CA CA P 102 O ASP A 548 1555 1555 2.48 LINK CA CA P 102 O LEU A 550 1555 1555 2.49 LINK CA CA P 102 O VAL A 553 1555 1555 2.48 LINK CA CA P 102 O HOH A1384 1555 1555 2.46 LINK OD1 ASP A 362 CA CA A 803 1555 1555 2.62 LINK OD2 ASP A 362 CA CA A 803 1555 1555 2.36 LINK O PHE A 363 CA CA A 803 1555 1555 2.33 LINK OD2 ASP A 467 CA CA A 803 1555 1555 2.34 LINK O2A DCP A 801 CA CA A 803 1555 1555 2.34 LINK O2B DCP A 801 CA CA A 803 1555 1555 2.32 LINK O3G DCP A 801 CA CA A 803 1555 1555 2.43 CISPEP 1 LYS A 525 PRO A 526 0 -3.93 SITE 1 AC1 7 ASP A 362 ASP A 467 GLU A 468 DCP A 801 SITE 2 AC1 7 CA A 803 HOH A1197 DG P 12 SITE 1 AC2 6 ASP A 548 LEU A 550 VAL A 553 HOH A1384 SITE 2 AC2 6 DA P 11 HOH P 219 SITE 1 AC3 26 ARG A 324 LEU A 328 ASP A 362 PHE A 363 SITE 2 AC3 26 ASP A 364 CYS A 365 PHE A 366 PHE A 367 SITE 3 AC3 26 ALA A 401 SER A 402 TYR A 405 ARG A 408 SITE 4 AC3 26 ASN A 414 ASP A 467 LYS A 525 GOL A 802 SITE 5 AC3 26 CA A 803 HOH A1029 HOH A1030 HOH A1079 SITE 6 AC3 26 HOH A1111 HOH A1124 HOH A1207 HOH A1248 SITE 7 AC3 26 DG P 12 CA P 101 SITE 1 AC4 9 ARG A 324 ASP A 399 GLY A 415 DCP A 801 SITE 2 AC4 9 HOH A1017 DG P 12 HOH P 216 HOH P 221 SITE 3 AC4 9 HOH P 228 SITE 1 AC5 5 ASP A 362 PHE A 363 ASP A 467 DCP A 801 SITE 2 AC5 5 CA P 101 CRYST1 62.376 73.947 117.290 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 0.016032 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008526 0.00000