HEADER TRANSFERASE 29-FEB-16 5IHE TITLE D-FAMILY DNA POLYMERASE - DP1 SUBUNIT (3'-5' PROOF-READING TITLE 2 EXONUCLEASE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE II SMALL SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: POL II; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI (STRAIN GE5 / ORSAY); SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 GENE: POLB, PYRAB01210, PAB2266; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE D-FAMILY EXONUCLEASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.SAUGUET,P.RAIA,M.DE LARUE REVDAT 3 08-MAY-24 5IHE 1 LINK REVDAT 2 07-SEP-16 5IHE 1 JRNL REVDAT 1 31-AUG-16 5IHE 0 JRNL AUTH L.SAUGUET,P.RAIA,G.HENNEKE,M.DELARUE JRNL TITL SHARED ACTIVE SITE ARCHITECTURE BETWEEN ARCHAEAL POLD AND JRNL TITL 2 MULTI-SUBUNIT RNA POLYMERASES REVEALED BY X-RAY JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF NAT COMMUN V. 7 12227 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27548043 JRNL DOI 10.1038/NCOMMS12227 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 39885 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.56 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.53 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2933 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2395 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2804 REMARK 3 BIN R VALUE (WORKING SET) : 0.2395 REMARK 3 BIN FREE R VALUE : 0.2398 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 129 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 81.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.64180 REMARK 3 B22 (A**2) : -5.15970 REMARK 3 B33 (A**2) : 10.80140 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.360 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.380 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.233 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.396 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.239 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 7283 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 9902 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2487 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 177 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1056 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 7283 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 924 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 8075 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.08 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.86 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.81 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 67.7280 72.5160 46.3622 REMARK 3 T TENSOR REMARK 3 T11: -0.1640 T22: 0.0054 REMARK 3 T33: -0.2946 T12: 0.0609 REMARK 3 T13: 0.0326 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.7653 L22: 1.9724 REMARK 3 L33: 2.9238 L12: 0.3466 REMARK 3 L13: 0.6831 L23: -0.7745 REMARK 3 S TENSOR REMARK 3 S11: -0.3023 S12: 0.2307 S13: -0.0158 REMARK 3 S21: -0.2413 S22: 0.1653 S23: 0.0900 REMARK 3 S31: -0.1780 S32: 0.0667 S33: 0.1371 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 43.8569 43.0610 74.5925 REMARK 3 T TENSOR REMARK 3 T11: -0.2313 T22: -0.2249 REMARK 3 T33: -0.1129 T12: 0.0648 REMARK 3 T13: 0.0894 T23: 0.0847 REMARK 3 L TENSOR REMARK 3 L11: 2.4121 L22: 1.9555 REMARK 3 L33: 2.3288 L12: -0.2365 REMARK 3 L13: 0.5881 L23: 0.4673 REMARK 3 S TENSOR REMARK 3 S11: -0.0920 S12: -0.1492 S13: -0.4123 REMARK 3 S21: -0.0978 S22: -0.0713 S23: -0.2607 REMARK 3 S31: 0.1903 S32: 0.1480 S33: 0.1633 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5IHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9919 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39885 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 48.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 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) : 0.82500 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA CACODYLATE PH6.7 200MM CA REMARK 280 ACETATE 5% PEG8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 42.98450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.60450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.70750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.60450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.98450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.70750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 145 REMARK 465 GLU A 146 REMARK 465 ASN A 147 REMARK 465 GLY A 148 REMARK 465 GLU A 149 REMARK 465 SER A 150 REMARK 465 VAL A 151 REMARK 465 ALA A 164 REMARK 465 PRO A 165 REMARK 465 GLU A 166 REMARK 465 GLU A 167 REMARK 465 ILE A 168 REMARK 465 GLY A 169 REMARK 465 GLU A 170 REMARK 465 GLU A 171 REMARK 465 LYS A 172 REMARK 465 GLU A 173 REMARK 465 LYS A 207 REMARK 465 LEU A 208 REMARK 465 ARG A 209 REMARK 465 PRO A 210 REMARK 465 PRO A 211 REMARK 465 LYS A 212 REMARK 465 VAL A 213 REMARK 465 LYS A 214 REMARK 465 ASN A 215 REMARK 465 GLY A 216 REMARK 465 SER A 217 REMARK 465 GLY A 218 REMARK 465 LYS A 219 REMARK 465 GLU A 220 REMARK 465 GLY A 221 REMARK 465 GLU A 222 REMARK 465 ILE A 223 REMARK 465 ILE A 224 REMARK 465 GLY B 145 REMARK 465 GLU B 146 REMARK 465 ASN B 147 REMARK 465 GLY B 148 REMARK 465 GLU B 149 REMARK 465 SER B 150 REMARK 465 VAL B 151 REMARK 465 ALA B 164 REMARK 465 PRO B 165 REMARK 465 GLU B 166 REMARK 465 GLU B 167 REMARK 465 ILE B 168 REMARK 465 GLY B 169 REMARK 465 GLU B 170 REMARK 465 GLU B 171 REMARK 465 LYS B 172 REMARK 465 GLU B 173 REMARK 465 VAL B 213 REMARK 465 LYS B 214 REMARK 465 ASN B 215 REMARK 465 GLY B 216 REMARK 465 SER B 217 REMARK 465 GLY B 218 REMARK 465 LYS B 219 REMARK 465 GLU B 220 REMARK 465 GLY B 221 REMARK 465 GLU B 222 REMARK 465 ILE B 223 REMARK 465 ILE B 224 REMARK 465 LEU B 511 REMARK 465 THR B 512 REMARK 465 HIS B 513 REMARK 465 HIS B 514 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 LYS A 156 CG CD CE NZ REMARK 470 TYR A 157 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 156 CG CD CE NZ REMARK 470 TYR B 157 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 515 CG CD CE NZ 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 LYS A 325 4.69 84.48 REMARK 500 ASP A 338 -166.31 58.24 REMARK 500 ALA A 402 58.44 -93.41 REMARK 500 PRO A 422 39.98 -92.03 REMARK 500 PRO A 456 37.02 -81.16 REMARK 500 GLU A 462 -159.67 -163.68 REMARK 500 HIS A 514 -14.60 73.47 REMARK 500 LYS A 515 71.60 -153.20 REMARK 500 ALA A 530 80.21 -155.42 REMARK 500 VAL A 537 91.15 -69.66 REMARK 500 HIS A 560 -52.95 65.70 REMARK 500 ALA A 578 -129.19 56.91 REMARK 500 GLN B 205 156.06 -42.18 REMARK 500 ASP B 301 34.40 -95.16 REMARK 500 ASP B 338 -165.03 61.81 REMARK 500 ALA B 402 58.28 -93.03 REMARK 500 PRO B 422 40.00 -91.81 REMARK 500 PRO B 456 30.27 -78.28 REMARK 500 GLU B 462 -159.83 -178.18 REMARK 500 ALA B 530 79.75 -155.35 REMARK 500 HIS B 560 -53.16 65.45 REMARK 500 ALA B 578 -129.37 56.55 REMARK 500 TRP B 618 30.82 -86.81 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 FE A 702 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 360 OD1 REMARK 620 2 HIS A 362 NE2 113.3 REMARK 620 3 ASP A 404 OD2 82.8 101.1 REMARK 620 4 HIS A 562 NE2 91.3 88.9 169.7 REMARK 620 5 D5M A 701 O1P 125.3 118.6 71.8 105.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 404 OD2 REMARK 620 2 ASN A 450 OD1 103.4 REMARK 620 3 HIS A 497 NE2 78.9 87.7 REMARK 620 4 HIS A 560 ND1 163.6 91.6 95.4 REMARK 620 5 D5M A 701 O1P 71.1 127.3 137.8 105.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 702 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 360 OD1 REMARK 620 2 HIS B 362 NE2 111.4 REMARK 620 3 ASP B 404 OD2 90.4 92.8 REMARK 620 4 HIS B 562 NE2 91.1 88.9 177.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 404 OD2 REMARK 620 2 ASN B 450 OD1 100.1 REMARK 620 3 HIS B 497 NE2 90.6 89.7 REMARK 620 4 HIS B 560 ND1 165.3 91.1 99.0 REMARK 620 5 D5M B 701 O1P 80.8 101.2 167.1 87.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D5M A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D5M B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 706 DBREF 5IHE A 145 619 UNP Q9V2F3 DP2S_PYRAB 145 619 DBREF 5IHE B 145 619 UNP Q9V2F3 DP2S_PYRAB 145 619 SEQRES 1 A 475 GLY GLU ASN GLY GLU SER VAL VAL VAL LEU ASP LYS TYR SEQRES 2 A 475 GLY TYR PRO ILE LEU TYR ALA PRO GLU GLU ILE GLY GLU SEQRES 3 A 475 GLU LYS GLU TYR SER LYS TYR GLU ASP VAL VAL ILE GLU SEQRES 4 A 475 TRP ASN PRO SER VAL THR PRO VAL GLN ILE GLU LYS ASN SEQRES 5 A 475 TYR GLU VAL LYS PHE ASP VAL ARG GLN VAL LYS LEU ARG SEQRES 6 A 475 PRO PRO LYS VAL LYS ASN GLY SER GLY LYS GLU GLY GLU SEQRES 7 A 475 ILE ILE VAL GLU ALA TYR ALA SER LEU PHE LYS SER ARG SEQRES 8 A 475 LEU SER LYS LEU LYS ARG ILE LEU ARG GLU ASN PRO GLU SEQRES 9 A 475 ILE SER ASN VAL VAL ASP ILE GLY LYS LEU ASN TYR VAL SEQRES 10 A 475 SER GLY ASP GLU GLU VAL THR ILE ILE GLY LEU VAL ASN SEQRES 11 A 475 SER LYS ARG GLU THR ASN ARG GLY LEU ILE PHE GLU VAL SEQRES 12 A 475 GLU ASP LYS THR GLY ILE VAL LYS VAL PHE LEU PRO LYS SEQRES 13 A 475 ASP SER GLU ASP TYR ARG GLU ALA PHE LYS VAL LEU PRO SEQRES 14 A 475 ASP ALA VAL VAL ALA PHE LYS GLY PHE TYR SER LYS LYS SEQRES 15 A 475 GLY ILE PHE PHE ALA ASN LYS PHE TYR LEU PRO ASP VAL SEQRES 16 A 475 PRO LEU TYR ARG LYS GLN LYS PRO PRO LEU GLU GLU LYS SEQRES 17 A 475 VAL TYR ALA ILE LEU ILE SER ASP ILE HIS VAL GLY SER SEQRES 18 A 475 ARG GLU PHE CYS GLU LYS ALA PHE LEU LYS PHE LEU GLU SEQRES 19 A 475 TRP LEU ASN GLY HIS VAL GLU SER LYS GLU GLU GLU GLU SEQRES 20 A 475 ILE VAL SER ARG VAL LYS TYR LEU ILE ILE ALA GLY ASP SEQRES 21 A 475 VAL VAL ASP GLY ILE GLY ILE TYR PRO GLY GLN TYR SER SEQRES 22 A 475 ASP LEU VAL ILE PRO ASP ILE PHE ASP GLN TYR GLU ALA SEQRES 23 A 475 LEU ALA ASN LEU LEU ALA ASN VAL PRO GLU HIS ILE THR SEQRES 24 A 475 MET PHE ILE GLY PRO GLY ASN HIS ASP ALA ALA ARG PRO SEQRES 25 A 475 ALA ILE PRO GLN PRO GLU PHE TYR LYS GLU TYR ALA LYS SEQRES 26 A 475 PRO ILE TYR LYS LEU LYS ASN ALA ILE ILE ILE SER ASN SEQRES 27 A 475 PRO ALA VAL ILE ARG LEU HIS GLY ARG ASP PHE LEU ILE SEQRES 28 A 475 ALA HIS GLY ARG GLY ILE GLU ASP VAL VAL SER PHE VAL SEQRES 29 A 475 PRO GLY LEU THR HIS HIS LYS PRO GLY LEU PRO MET VAL SEQRES 30 A 475 GLU LEU LEU LYS MET ARG HIS LEU ALA PRO THR PHE GLY SEQRES 31 A 475 GLY LYS VAL PRO ILE ALA PRO ASP PRO GLU ASP LEU LEU SEQRES 32 A 475 VAL ILE GLU GLU VAL PRO ASP LEU VAL GLN MET GLY HIS SEQRES 33 A 475 VAL HIS VAL TYR ASP ALA VAL VAL TYR ARG GLY VAL GLN SEQRES 34 A 475 LEU VAL ASN SER ALA THR TRP GLN ALA GLN THR GLU PHE SEQRES 35 A 475 GLN LYS MET VAL ASN ILE VAL PRO THR PRO ALA LYS VAL SEQRES 36 A 475 PRO VAL VAL ASP VAL GLU SER ALA ARG VAL VAL LYS VAL SEQRES 37 A 475 LEU ASP PHE SER GLY TRP CYS SEQRES 1 B 475 GLY GLU ASN GLY GLU SER VAL VAL VAL LEU ASP LYS TYR SEQRES 2 B 475 GLY TYR PRO ILE LEU TYR ALA PRO GLU GLU ILE GLY GLU SEQRES 3 B 475 GLU LYS GLU TYR SER LYS TYR GLU ASP VAL VAL ILE GLU SEQRES 4 B 475 TRP ASN PRO SER VAL THR PRO VAL GLN ILE GLU LYS ASN SEQRES 5 B 475 TYR GLU VAL LYS PHE ASP VAL ARG GLN VAL LYS LEU ARG SEQRES 6 B 475 PRO PRO LYS VAL LYS ASN GLY SER GLY LYS GLU GLY GLU SEQRES 7 B 475 ILE ILE VAL GLU ALA TYR ALA SER LEU PHE LYS SER ARG SEQRES 8 B 475 LEU SER LYS LEU LYS ARG ILE LEU ARG GLU ASN PRO GLU SEQRES 9 B 475 ILE SER ASN VAL VAL ASP ILE GLY LYS LEU ASN TYR VAL SEQRES 10 B 475 SER GLY ASP GLU GLU VAL THR ILE ILE GLY LEU VAL ASN SEQRES 11 B 475 SER LYS ARG GLU THR ASN ARG GLY LEU ILE PHE GLU VAL SEQRES 12 B 475 GLU ASP LYS THR GLY ILE VAL LYS VAL PHE LEU PRO LYS SEQRES 13 B 475 ASP SER GLU ASP TYR ARG GLU ALA PHE LYS VAL LEU PRO SEQRES 14 B 475 ASP ALA VAL VAL ALA PHE LYS GLY PHE TYR SER LYS LYS SEQRES 15 B 475 GLY ILE PHE PHE ALA ASN LYS PHE TYR LEU PRO ASP VAL SEQRES 16 B 475 PRO LEU TYR ARG LYS GLN LYS PRO PRO LEU GLU GLU LYS SEQRES 17 B 475 VAL TYR ALA ILE LEU ILE SER ASP ILE HIS VAL GLY SER SEQRES 18 B 475 ARG GLU PHE CYS GLU LYS ALA PHE LEU LYS PHE LEU GLU SEQRES 19 B 475 TRP LEU ASN GLY HIS VAL GLU SER LYS GLU GLU GLU GLU SEQRES 20 B 475 ILE VAL SER ARG VAL LYS TYR LEU ILE ILE ALA GLY ASP SEQRES 21 B 475 VAL VAL ASP GLY ILE GLY ILE TYR PRO GLY GLN TYR SER SEQRES 22 B 475 ASP LEU VAL ILE PRO ASP ILE PHE ASP GLN TYR GLU ALA SEQRES 23 B 475 LEU ALA ASN LEU LEU ALA ASN VAL PRO GLU HIS ILE THR SEQRES 24 B 475 MET PHE ILE GLY PRO GLY ASN HIS ASP ALA ALA ARG PRO SEQRES 25 B 475 ALA ILE PRO GLN PRO GLU PHE TYR LYS GLU TYR ALA LYS SEQRES 26 B 475 PRO ILE TYR LYS LEU LYS ASN ALA ILE ILE ILE SER ASN SEQRES 27 B 475 PRO ALA VAL ILE ARG LEU HIS GLY ARG ASP PHE LEU ILE SEQRES 28 B 475 ALA HIS GLY ARG GLY ILE GLU ASP VAL VAL SER PHE VAL SEQRES 29 B 475 PRO GLY LEU THR HIS HIS LYS PRO GLY LEU PRO MET VAL SEQRES 30 B 475 GLU LEU LEU LYS MET ARG HIS LEU ALA PRO THR PHE GLY SEQRES 31 B 475 GLY LYS VAL PRO ILE ALA PRO ASP PRO GLU ASP LEU LEU SEQRES 32 B 475 VAL ILE GLU GLU VAL PRO ASP LEU VAL GLN MET GLY HIS SEQRES 33 B 475 VAL HIS VAL TYR ASP ALA VAL VAL TYR ARG GLY VAL GLN SEQRES 34 B 475 LEU VAL ASN SER ALA THR TRP GLN ALA GLN THR GLU PHE SEQRES 35 B 475 GLN LYS MET VAL ASN ILE VAL PRO THR PRO ALA LYS VAL SEQRES 36 B 475 PRO VAL VAL ASP VAL GLU SER ALA ARG VAL VAL LYS VAL SEQRES 37 B 475 LEU ASP PHE SER GLY TRP CYS HET D5M A 701 22 HET FE A 702 1 HET ZN A 703 1 HET CA A 704 1 HET ACT A 705 4 HET CA A 706 1 HET D5M B 701 22 HET FE B 702 1 HET ZN B 703 1 HET CA B 704 1 HET ACT B 705 4 HET EDO B 706 4 HETNAM D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM FE FE (III) ION HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 D5M 2(C10 H14 N5 O6 P) FORMUL 4 FE 2(FE 3+) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 CA 3(CA 2+) FORMUL 7 ACT 2(C2 H3 O2 1-) FORMUL 14 EDO C2 H6 O2 FORMUL 15 HOH *66(H2 O) HELIX 1 AA1 ASP A 202 VAL A 206 5 5 HELIX 2 AA2 TYR A 228 ARG A 244 1 17 HELIX 3 AA3 ASP A 254 LEU A 258 5 5 HELIX 4 AA4 ASP A 304 VAL A 311 1 8 HELIX 5 AA5 CYS A 369 ASN A 381 1 13 HELIX 6 AA6 SER A 386 SER A 394 1 9 HELIX 7 AA7 GLY A 414 LEU A 419 5 6 HELIX 8 AA8 ASP A 423 ALA A 436 1 14 HELIX 9 AA9 TYR A 464 LYS A 473 1 10 HELIX 10 AB1 GLY A 498 VAL A 508 1 11 HELIX 11 AB2 PRO A 516 ARG A 527 1 12 HELIX 12 AB3 THR A 584 VAL A 590 1 7 HELIX 13 AB4 SER A 616 CYS A 619 5 4 HELIX 14 AB5 TYR B 228 ARG B 244 1 17 HELIX 15 AB6 ASP B 254 VAL B 261 5 8 HELIX 16 AB7 ASP B 304 VAL B 311 1 8 HELIX 17 AB8 CYS B 369 ASN B 381 1 13 HELIX 18 AB9 SER B 386 ARG B 395 1 10 HELIX 19 AC1 GLY B 414 LEU B 419 5 6 HELIX 20 AC2 ASP B 423 ALA B 436 1 14 HELIX 21 AC3 TYR B 464 LYS B 473 1 10 HELIX 22 AC4 GLY B 498 VAL B 508 1 11 HELIX 23 AC5 PRO B 516 ARG B 527 1 12 HELIX 24 AC6 THR B 584 VAL B 590 1 7 HELIX 25 AC7 SER B 616 CYS B 619 5 4 SHEET 1 AA1 2 LEU A 154 LYS A 156 0 SHEET 2 AA1 2 TYR A 159 LEU A 162 -1 O LEU A 162 N LEU A 154 SHEET 1 AA2 6 TYR A 197 PHE A 201 0 SHEET 2 AA2 6 ALA A 484 LEU A 488 -1 O ARG A 487 N GLU A 198 SHEET 3 AA2 6 ARG A 491 ILE A 495 -1 O ILE A 495 N ALA A 484 SHEET 4 AA2 6 LEU A 555 MET A 558 1 O LEU A 555 N LEU A 494 SHEET 5 AA2 6 VAL A 572 SER A 577 1 O GLN A 573 N VAL A 556 SHEET 6 AA2 6 TYR A 564 TYR A 569 -1 N VAL A 567 O LEU A 574 SHEET 1 AA3 6 VAL A 267 THR A 279 0 SHEET 2 AA3 6 GLY A 282 GLU A 288 -1 O ILE A 284 N ARG A 277 SHEET 3 AA3 6 ILE A 293 PRO A 299 -1 O VAL A 296 N PHE A 285 SHEET 4 AA3 6 ILE A 328 TYR A 335 1 O PHE A 329 N LYS A 295 SHEET 5 AA3 6 VAL A 316 TYR A 323 -1 N LYS A 320 O ASN A 332 SHEET 6 AA3 6 VAL A 267 THR A 279 -1 N GLY A 271 O VAL A 317 SHEET 1 AA4 7 ALA A 477 ILE A 479 0 SHEET 2 AA4 7 THR A 443 GLY A 447 1 N MET A 444 O ILE A 478 SHEET 3 AA4 7 VAL A 396 ALA A 402 1 N ILE A 401 O PHE A 445 SHEET 4 AA4 7 TYR A 354 ILE A 358 1 N ILE A 358 O ILE A 400 SHEET 5 AA4 7 LYS A 598 ASP A 603 -1 O VAL A 602 N ALA A 355 SHEET 6 AA4 7 ARG A 608 ASP A 614 -1 O LEU A 613 N VAL A 599 SHEET 7 AA4 7 LYS B 207 ARG B 209 -1 O ARG B 209 N VAL A 612 SHEET 1 AA5 2 LEU B 154 LYS B 156 0 SHEET 2 AA5 2 TYR B 159 LEU B 162 -1 O LEU B 162 N LEU B 154 SHEET 1 AA6 6 TYR B 197 PHE B 201 0 SHEET 2 AA6 6 ALA B 484 LEU B 488 -1 O ARG B 487 N GLU B 198 SHEET 3 AA6 6 ARG B 491 ILE B 495 -1 O ILE B 495 N ALA B 484 SHEET 4 AA6 6 LEU B 555 MET B 558 1 O LEU B 555 N LEU B 494 SHEET 5 AA6 6 VAL B 572 SER B 577 1 O GLN B 573 N VAL B 556 SHEET 6 AA6 6 TYR B 564 TYR B 569 -1 N VAL B 567 O LEU B 574 SHEET 1 AA7 6 VAL B 267 GLU B 278 0 SHEET 2 AA7 6 GLY B 282 GLU B 288 -1 O ILE B 284 N ARG B 277 SHEET 3 AA7 6 ILE B 293 PRO B 299 -1 O VAL B 296 N PHE B 285 SHEET 4 AA7 6 ILE B 328 TYR B 335 1 O PHE B 329 N PHE B 297 SHEET 5 AA7 6 VAL B 316 TYR B 323 -1 N LYS B 320 O ASN B 332 SHEET 6 AA7 6 VAL B 267 GLU B 278 -1 N GLY B 271 O VAL B 317 SHEET 1 AA8 6 ALA B 477 ILE B 479 0 SHEET 2 AA8 6 THR B 443 GLY B 447 1 N MET B 444 O ILE B 478 SHEET 3 AA8 6 VAL B 396 ALA B 402 1 N ILE B 401 O PHE B 445 SHEET 4 AA8 6 TYR B 354 ILE B 358 1 N ILE B 358 O ILE B 400 SHEET 5 AA8 6 LYS B 598 ASP B 603 -1 O VAL B 602 N ALA B 355 SHEET 6 AA8 6 ARG B 608 ASP B 614 -1 O LYS B 611 N VAL B 601 LINK OD1 ASP A 360 FE FE A 702 1555 1555 1.94 LINK NE2 HIS A 362 FE FE A 702 1555 1555 2.22 LINK O GLU A 385 CA CA A 706 1555 1555 3.09 LINK OD2 ASP A 404 FE FE A 702 1555 1555 2.54 LINK OD2 ASP A 404 ZN ZN A 703 1555 1555 2.10 LINK OD1 ASN A 450 ZN ZN A 703 1555 1555 2.15 LINK NE2 HIS A 497 ZN ZN A 703 1555 1555 2.29 LINK ND1 HIS A 560 ZN ZN A 703 1555 1555 2.25 LINK NE2 HIS A 562 FE FE A 702 1555 1555 2.24 LINK O1P D5M A 701 FE FE A 702 1555 1555 2.06 LINK O1P D5M A 701 ZN ZN A 703 1555 1555 2.55 LINK OD1 ASP B 360 FE FE B 702 1555 1555 1.97 LINK NE2 HIS B 362 FE FE B 702 1555 1555 2.25 LINK OD2 ASP B 404 FE FE B 702 1555 1555 2.48 LINK OD2 ASP B 404 ZN ZN B 703 1555 1555 2.33 LINK OD1 ASN B 450 ZN ZN B 703 1555 1555 2.19 LINK NE2 HIS B 497 ZN ZN B 703 1555 1555 2.17 LINK OE2 GLU B 544 CA CA B 704 1555 1555 2.61 LINK ND1 HIS B 560 ZN ZN B 703 1555 1555 2.25 LINK NE2 HIS B 562 FE FE B 702 1555 1555 2.21 LINK O1P D5M B 701 ZN ZN B 703 1555 1555 1.94 CISPEP 1 ILE A 458 PRO A 459 0 5.13 CISPEP 2 ASN A 482 PRO A 483 0 5.17 CISPEP 3 ILE B 458 PRO B 459 0 5.20 CISPEP 4 ASN B 482 PRO B 483 0 4.38 SITE 1 AC1 14 ASP A 360 HIS A 362 ASP A 404 ASN A 450 SITE 2 AC1 14 HIS A 451 GLU A 502 HIS A 560 VAL A 561 SITE 3 AC1 14 HIS A 562 PHE A 586 ILE A 592 FE A 702 SITE 4 AC1 14 ZN A 703 GLY B 534 SITE 1 AC2 6 ASP A 360 HIS A 362 ASP A 404 HIS A 562 SITE 2 AC2 6 D5M A 701 ZN A 703 SITE 1 AC3 6 ASP A 404 ASN A 450 HIS A 497 HIS A 560 SITE 2 AC3 6 D5M A 701 FE A 702 SITE 1 AC4 1 LYS A 588 SITE 1 AC5 6 ILE A 458 ASN A 482 HIS A 497 GLY A 498 SITE 2 AC5 6 ARG A 499 HOH A 805 SITE 1 AC6 3 GLU A 385 GLU B 550 GLU B 551 SITE 1 AC7 12 GLY A 534 HIS B 362 ASP B 404 ASN B 450 SITE 2 AC7 12 HIS B 451 GLU B 502 HIS B 560 VAL B 561 SITE 3 AC7 12 PHE B 586 ILE B 592 FE B 702 ZN B 703 SITE 1 AC8 6 ASP B 360 HIS B 362 ASP B 404 HIS B 562 SITE 2 AC8 6 D5M B 701 ZN B 703 SITE 1 AC9 6 ASP B 404 ASN B 450 HIS B 497 HIS B 560 SITE 2 AC9 6 D5M B 701 FE B 702 SITE 1 AD1 2 GLU B 544 GLU B 550 SITE 1 AD2 6 ILE B 458 ASN B 482 HIS B 497 GLY B 498 SITE 2 AD2 6 ARG B 499 HOH B 801 SITE 1 AD3 6 ASN B 450 ASP B 452 ALA B 454 ARG B 455 SITE 2 AD3 6 PRO B 456 GLN B 460 CRYST1 85.969 91.415 145.209 90.00 90.00 90.00 P 21 21 21 8 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 0.011632 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006887 0.00000