HEADER BIOSYNTHETIC PROTEIN 01-MAR-10 3LZD TITLE CRYSTAL STRUCTURE OF DPH2 FROM PYROCOCCUS HORIKOSHII WITH 4FE-4S TITLE 2 CLUSTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DPH2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDESTF1 KEYWDS DIPHTHAMIDE BIOSYNTHESIS, RADICAL SAM ENZYME, GENE TRIPLICATION, KEYWDS 2 IRON-SULFUR CLUSTER, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.T.TORELLI,Y.ZHANG,X.ZHU,M.LEE,B.DZIKOVSKI,R.M.KORALEWSKI,E.WANG, AUTHOR 2 J.FREED,C.KREBS,H.LIN,S.E.EALICK REVDAT 2 06-SEP-23 3LZD 1 REMARK SEQADV LINK REVDAT 1 14-JUL-10 3LZD 0 JRNL AUTH Y.ZHANG,X.ZHU,A.T.TORELLI,M.LEE,B.DZIKOVSKI,R.M.KORALEWSKI, JRNL AUTH 2 E.WANG,J.FREED,C.KREBS,S.E.EALICK,H.LIN JRNL TITL DIPHTHAMIDE BIOSYNTHESIS REQUIRES AN ORGANIC RADICAL JRNL TITL 2 GENERATED BY AN IRON-SULPHUR ENZYME. JRNL REF NATURE V. 465 891 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20559380 JRNL DOI 10.1038/NATURE09138 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 41054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RFREE SELECTION MATCHED (AND REMARK 3 EXTENDED) THAT OF THE REMARK 3 STARTING MODEL REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2066 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 5198 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 258 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 15.32000 REMARK 3 B22 (A**2) : 3.47900 REMARK 3 B33 (A**2) : -18.79900 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 55.93 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : SF4.PAR REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3LZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000057914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41054 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.06200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.24100 REMARK 200 R SYM FOR SHELL (I) : 0.24100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 3LZC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 400, 0.06 M 2-(N REMARK 280 -MORPHOLINO)ETHANESULFONIC ACID, 0.12 M LITHIUM SULFATE, 3% REMARK 280 ETHYLENE GLYCOL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 299K 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 27.84750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.07100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.26250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.07100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.84750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.26250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A -35 REMARK 465 GLY A -34 REMARK 465 SER A -33 REMARK 465 HIS A -32 REMARK 465 HIS A -31 REMARK 465 HIS A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 ASP A -26 REMARK 465 ILE A -25 REMARK 465 THR A -24 REMARK 465 SER A -23 REMARK 465 LEU A -22 REMARK 465 TYR A -21 REMARK 465 LYS A -20 REMARK 465 LYS A -19 REMARK 465 ALA A -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 ALA A -15 REMARK 465 ALA A -14 REMARK 465 ALA A -13 REMARK 465 VAL A -12 REMARK 465 LEU A -11 REMARK 465 GLU A -10 REMARK 465 GLU A -9 REMARK 465 ASN A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 PHE A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 PHE A -1 REMARK 465 THR A 0 REMARK 465 MET A 1 REMARK 465 ARG A 342 REMARK 465 MET B -35 REMARK 465 GLY B -34 REMARK 465 SER B -33 REMARK 465 HIS B -32 REMARK 465 HIS B -31 REMARK 465 HIS B -30 REMARK 465 HIS B -29 REMARK 465 HIS B -28 REMARK 465 HIS B -27 REMARK 465 ASP B -26 REMARK 465 ILE B -25 REMARK 465 THR B -24 REMARK 465 SER B -23 REMARK 465 LEU B -22 REMARK 465 TYR B -21 REMARK 465 LYS B -20 REMARK 465 LYS B -19 REMARK 465 ALA B -18 REMARK 465 GLY B -17 REMARK 465 SER B -16 REMARK 465 ALA B -15 REMARK 465 ALA B -14 REMARK 465 ALA B -13 REMARK 465 VAL B -12 REMARK 465 LEU B -11 REMARK 465 GLU B -10 REMARK 465 GLU B -9 REMARK 465 ASN B -8 REMARK 465 LEU B -7 REMARK 465 TYR B -6 REMARK 465 PHE B -5 REMARK 465 GLN B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 PHE B -1 REMARK 465 THR B 0 REMARK 465 ASP B 294 REMARK 465 TYR B 295 REMARK 465 GLY B 296 REMARK 465 ALA B 297 REMARK 465 ARG B 342 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 GLU A 4 CG CD OE1 OE2 REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 GLU A 28 CG CD OE1 OE2 REMARK 470 GLU A 36 CG CD OE1 OE2 REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 LYS A 106 CG CD CE NZ REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 195 CG CD CE NZ REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 217 CG CD CE NZ REMARK 470 ASP A 227 CG OD1 OD2 REMARK 470 LYS A 229 CG CD CE NZ REMARK 470 LYS A 252 CG CD CE NZ REMARK 470 LYS A 256 CG CD CE NZ REMARK 470 GLU A 275 CG CD OE1 OE2 REMARK 470 GLU A 316 CG CD OE1 OE2 REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 GLU B 4 CG CD OE1 OE2 REMARK 470 LYS B 12 CG CD CE NZ REMARK 470 ARG B 16 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 20 CG CD CE NZ REMARK 470 GLU B 28 CG CD OE1 OE2 REMARK 470 ARG B 32 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 98 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 ARG B 213 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 217 CG CD CE NZ REMARK 470 LYS B 229 CG CD CE NZ REMARK 470 ARG B 299 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 300 CG CD CE NZ REMARK 470 GLU B 317 CG CD OE1 OE2 REMARK 470 GLU B 329 CG CD OE1 OE2 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 VAL A 93 79.95 -119.40 REMARK 500 ASN A 267 -86.13 -110.04 REMARK 500 VAL A 285 69.20 -115.21 REMARK 500 ALA A 286 -114.18 -154.69 REMARK 500 ASP A 293 38.29 -140.59 REMARK 500 PHE A 334 76.35 -101.07 REMARK 500 SER A 340 114.69 -160.59 REMARK 500 ALA B 62 40.58 -96.85 REMARK 500 LYS B 83 108.76 -55.11 REMARK 500 ASP B 151 -164.25 -113.50 REMARK 500 ASN B 267 -79.28 -114.13 REMARK 500 VAL B 285 73.97 -117.24 REMARK 500 ALA B 286 -121.73 -160.33 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 SF4 A 343 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 59 SG REMARK 620 2 SF4 A 343 S1 117.1 REMARK 620 3 SF4 A 343 S2 114.9 102.7 REMARK 620 4 SF4 A 343 S3 112.7 104.7 103.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 343 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 163 SG REMARK 620 2 SF4 A 343 S1 129.9 REMARK 620 3 SF4 A 343 S2 102.9 103.0 REMARK 620 4 SF4 A 343 S4 108.4 104.9 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 343 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 287 SG REMARK 620 2 SF4 A 343 S2 112.3 REMARK 620 3 SF4 A 343 S3 122.5 103.5 REMARK 620 4 SF4 A 343 S4 110.3 103.3 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 343 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 59 SG REMARK 620 2 SF4 B 343 S1 112.6 REMARK 620 3 SF4 B 343 S2 115.1 103.6 REMARK 620 4 SF4 B 343 S3 115.1 104.9 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 343 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 163 SG REMARK 620 2 SF4 B 343 S1 127.0 REMARK 620 3 SF4 B 343 S2 106.6 103.8 REMARK 620 4 SF4 B 343 S4 107.6 104.6 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 343 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 287 SG REMARK 620 2 SF4 B 343 S2 110.5 REMARK 620 3 SF4 B 343 S3 118.8 103.6 REMARK 620 4 SF4 B 343 S4 116.7 102.4 102.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 345 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LZC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DPH2 FROM PYROCOCCUS HORIKOSHII DBREF 3LZD A 1 342 UNP O58832 O58832_PYRHO 1 342 DBREF 3LZD B 1 342 UNP O58832 O58832_PYRHO 1 342 SEQADV 3LZD MET A -35 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLY A -34 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER A -33 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS A -32 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS A -31 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS A -30 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS A -29 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS A -28 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS A -27 UNP O58832 EXPRESSION TAG SEQADV 3LZD ASP A -26 UNP O58832 EXPRESSION TAG SEQADV 3LZD ILE A -25 UNP O58832 EXPRESSION TAG SEQADV 3LZD THR A -24 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER A -23 UNP O58832 EXPRESSION TAG SEQADV 3LZD LEU A -22 UNP O58832 EXPRESSION TAG SEQADV 3LZD TYR A -21 UNP O58832 EXPRESSION TAG SEQADV 3LZD LYS A -20 UNP O58832 EXPRESSION TAG SEQADV 3LZD LYS A -19 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA A -18 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLY A -17 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER A -16 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA A -15 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA A -14 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA A -13 UNP O58832 EXPRESSION TAG SEQADV 3LZD VAL A -12 UNP O58832 EXPRESSION TAG SEQADV 3LZD LEU A -11 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLU A -10 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLU A -9 UNP O58832 EXPRESSION TAG SEQADV 3LZD ASN A -8 UNP O58832 EXPRESSION TAG SEQADV 3LZD LEU A -7 UNP O58832 EXPRESSION TAG SEQADV 3LZD TYR A -6 UNP O58832 EXPRESSION TAG SEQADV 3LZD PHE A -5 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLN A -4 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLY A -3 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER A -2 UNP O58832 EXPRESSION TAG SEQADV 3LZD PHE A -1 UNP O58832 EXPRESSION TAG SEQADV 3LZD THR A 0 UNP O58832 EXPRESSION TAG SEQADV 3LZD MET B -35 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLY B -34 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER B -33 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS B -32 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS B -31 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS B -30 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS B -29 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS B -28 UNP O58832 EXPRESSION TAG SEQADV 3LZD HIS B -27 UNP O58832 EXPRESSION TAG SEQADV 3LZD ASP B -26 UNP O58832 EXPRESSION TAG SEQADV 3LZD ILE B -25 UNP O58832 EXPRESSION TAG SEQADV 3LZD THR B -24 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER B -23 UNP O58832 EXPRESSION TAG SEQADV 3LZD LEU B -22 UNP O58832 EXPRESSION TAG SEQADV 3LZD TYR B -21 UNP O58832 EXPRESSION TAG SEQADV 3LZD LYS B -20 UNP O58832 EXPRESSION TAG SEQADV 3LZD LYS B -19 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA B -18 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLY B -17 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER B -16 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA B -15 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA B -14 UNP O58832 EXPRESSION TAG SEQADV 3LZD ALA B -13 UNP O58832 EXPRESSION TAG SEQADV 3LZD VAL B -12 UNP O58832 EXPRESSION TAG SEQADV 3LZD LEU B -11 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLU B -10 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLU B -9 UNP O58832 EXPRESSION TAG SEQADV 3LZD ASN B -8 UNP O58832 EXPRESSION TAG SEQADV 3LZD LEU B -7 UNP O58832 EXPRESSION TAG SEQADV 3LZD TYR B -6 UNP O58832 EXPRESSION TAG SEQADV 3LZD PHE B -5 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLN B -4 UNP O58832 EXPRESSION TAG SEQADV 3LZD GLY B -3 UNP O58832 EXPRESSION TAG SEQADV 3LZD SER B -2 UNP O58832 EXPRESSION TAG SEQADV 3LZD PHE B -1 UNP O58832 EXPRESSION TAG SEQADV 3LZD THR B 0 UNP O58832 EXPRESSION TAG SEQRES 1 A 378 MET GLY SER HIS HIS HIS HIS HIS HIS ASP ILE THR SER SEQRES 2 A 378 LEU TYR LYS LYS ALA GLY SER ALA ALA ALA VAL LEU GLU SEQRES 3 A 378 GLU ASN LEU TYR PHE GLN GLY SER PHE THR MET LEU HIS SEQRES 4 A 378 GLU ILE PRO LYS SER GLU ILE LEU LYS GLU LEU LYS ARG SEQRES 5 A 378 ILE GLY ALA LYS ARG VAL LEU ILE GLN SER PRO GLU GLY SEQRES 6 A 378 LEU ARG ARG GLU ALA GLU GLU LEU ALA GLY PHE LEU GLU SEQRES 7 A 378 GLU ASN ASN ILE GLU VAL PHE LEU HIS GLY GLU ILE ASN SEQRES 8 A 378 TYR GLY ALA CYS ASP PRO ALA ASP ARG GLU ALA LYS LEU SEQRES 9 A 378 VAL GLY CYS ASP ALA LEU ILE HIS LEU GLY HIS SER TYR SEQRES 10 A 378 MET LYS LEU PRO LEU GLU VAL PRO THR ILE PHE VAL PRO SEQRES 11 A 378 ALA PHE ALA ARG VAL SER VAL VAL GLU ALA LEU LYS GLU SEQRES 12 A 378 ASN ILE GLY GLU ILE LYS LYS LEU GLY ARG LYS ILE ILE SEQRES 13 A 378 VAL THR THR THR ALA GLN HIS ILE HIS GLN LEU LYS GLU SEQRES 14 A 378 ALA LYS GLU PHE LEU GLU SER GLU GLY PHE GLU VAL SER SEQRES 15 A 378 ILE GLY ARG GLY ASP SER ARG ILE SER TRP PRO GLY GLN SEQRES 16 A 378 VAL LEU GLY CYS ASN TYR SER VAL ALA LYS VAL ARG GLY SEQRES 17 A 378 GLU GLY ILE LEU PHE ILE GLY SER GLY ILE PHE HIS PRO SEQRES 18 A 378 LEU GLY LEU ALA VAL ALA THR ARG LYS LYS VAL LEU ALA SEQRES 19 A 378 ILE ASP PRO TYR THR LYS ALA PHE SER TRP ILE ASP PRO SEQRES 20 A 378 GLU ARG PHE ILE ARG LYS ARG TRP ALA GLN ILE ALA LYS SEQRES 21 A 378 ALA MET ASP ALA LYS LYS PHE GLY VAL ILE VAL SER ILE SEQRES 22 A 378 LYS LYS GLY GLN LEU ARG LEU ALA GLU ALA LYS ARG ILE SEQRES 23 A 378 VAL LYS LEU LEU LYS LYS HIS GLY ARG GLU ALA ARG LEU SEQRES 24 A 378 ILE VAL MET ASN ASP VAL ASN TYR HIS LYS LEU GLU GLY SEQRES 25 A 378 PHE PRO PHE GLU ALA TYR VAL VAL VAL ALA CYS PRO ARG SEQRES 26 A 378 VAL PRO LEU ASP ASP TYR GLY ALA TRP ARG LYS PRO VAL SEQRES 27 A 378 LEU THR PRO LYS GLU VAL GLU ILE LEU LEU GLY LEU ARG SEQRES 28 A 378 GLU GLU TYR GLU PHE ASP GLU ILE LEU GLY GLY PRO ARG SEQRES 29 A 378 GLU SER ASP GLU PRO PHE GLY ILE SER ILE HIS SER THR SEQRES 30 A 378 ARG SEQRES 1 B 378 MET GLY SER HIS HIS HIS HIS HIS HIS ASP ILE THR SER SEQRES 2 B 378 LEU TYR LYS LYS ALA GLY SER ALA ALA ALA VAL LEU GLU SEQRES 3 B 378 GLU ASN LEU TYR PHE GLN GLY SER PHE THR MET LEU HIS SEQRES 4 B 378 GLU ILE PRO LYS SER GLU ILE LEU LYS GLU LEU LYS ARG SEQRES 5 B 378 ILE GLY ALA LYS ARG VAL LEU ILE GLN SER PRO GLU GLY SEQRES 6 B 378 LEU ARG ARG GLU ALA GLU GLU LEU ALA GLY PHE LEU GLU SEQRES 7 B 378 GLU ASN ASN ILE GLU VAL PHE LEU HIS GLY GLU ILE ASN SEQRES 8 B 378 TYR GLY ALA CYS ASP PRO ALA ASP ARG GLU ALA LYS LEU SEQRES 9 B 378 VAL GLY CYS ASP ALA LEU ILE HIS LEU GLY HIS SER TYR SEQRES 10 B 378 MET LYS LEU PRO LEU GLU VAL PRO THR ILE PHE VAL PRO SEQRES 11 B 378 ALA PHE ALA ARG VAL SER VAL VAL GLU ALA LEU LYS GLU SEQRES 12 B 378 ASN ILE GLY GLU ILE LYS LYS LEU GLY ARG LYS ILE ILE SEQRES 13 B 378 VAL THR THR THR ALA GLN HIS ILE HIS GLN LEU LYS GLU SEQRES 14 B 378 ALA LYS GLU PHE LEU GLU SER GLU GLY PHE GLU VAL SER SEQRES 15 B 378 ILE GLY ARG GLY ASP SER ARG ILE SER TRP PRO GLY GLN SEQRES 16 B 378 VAL LEU GLY CYS ASN TYR SER VAL ALA LYS VAL ARG GLY SEQRES 17 B 378 GLU GLY ILE LEU PHE ILE GLY SER GLY ILE PHE HIS PRO SEQRES 18 B 378 LEU GLY LEU ALA VAL ALA THR ARG LYS LYS VAL LEU ALA SEQRES 19 B 378 ILE ASP PRO TYR THR LYS ALA PHE SER TRP ILE ASP PRO SEQRES 20 B 378 GLU ARG PHE ILE ARG LYS ARG TRP ALA GLN ILE ALA LYS SEQRES 21 B 378 ALA MET ASP ALA LYS LYS PHE GLY VAL ILE VAL SER ILE SEQRES 22 B 378 LYS LYS GLY GLN LEU ARG LEU ALA GLU ALA LYS ARG ILE SEQRES 23 B 378 VAL LYS LEU LEU LYS LYS HIS GLY ARG GLU ALA ARG LEU SEQRES 24 B 378 ILE VAL MET ASN ASP VAL ASN TYR HIS LYS LEU GLU GLY SEQRES 25 B 378 PHE PRO PHE GLU ALA TYR VAL VAL VAL ALA CYS PRO ARG SEQRES 26 B 378 VAL PRO LEU ASP ASP TYR GLY ALA TRP ARG LYS PRO VAL SEQRES 27 B 378 LEU THR PRO LYS GLU VAL GLU ILE LEU LEU GLY LEU ARG SEQRES 28 B 378 GLU GLU TYR GLU PHE ASP GLU ILE LEU GLY GLY PRO ARG SEQRES 29 B 378 GLU SER ASP GLU PRO PHE GLY ILE SER ILE HIS SER THR SEQRES 30 B 378 ARG HET SF4 A 343 8 HET SO4 A 344 5 HET SF4 B 343 8 HET SO4 B 344 5 HET SO4 B 345 5 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM SO4 SULFATE ION FORMUL 3 SF4 2(FE4 S4) FORMUL 4 SO4 3(O4 S 2-) FORMUL 8 HOH *258(H2 O) HELIX 1 1 PRO A 6 ILE A 17 1 12 HELIX 2 2 PRO A 27 GLY A 29 5 3 HELIX 3 3 LEU A 30 GLU A 43 1 14 HELIX 4 4 ALA A 62 VAL A 69 1 8 HELIX 5 5 VAL A 101 ASN A 108 1 8 HELIX 6 6 ASN A 108 LYS A 114 1 7 HELIX 7 7 ALA A 125 HIS A 129 5 5 HELIX 8 8 GLN A 130 GLU A 141 1 12 HELIX 9 9 TYR A 165 LYS A 169 5 5 HELIX 10 10 ILE A 182 ARG A 193 1 12 HELIX 11 11 PRO A 211 MET A 226 1 16 HELIX 12 12 ARG A 243 HIS A 257 1 15 HELIX 13 13 ASN A 270 GLU A 275 1 6 HELIX 14 14 PRO A 288 ASP A 293 1 6 HELIX 15 15 THR A 304 LEU A 312 1 9 HELIX 16 16 PRO B 6 GLY B 18 1 13 HELIX 17 17 PRO B 27 GLY B 29 5 3 HELIX 18 18 LEU B 30 GLU B 43 1 14 HELIX 19 19 ALA B 62 VAL B 69 1 8 HELIX 20 20 SER B 100 ASN B 108 1 9 HELIX 21 21 ASN B 108 LYS B 114 1 7 HELIX 22 22 ALA B 125 HIS B 129 5 5 HELIX 23 23 GLN B 130 GLU B 141 1 12 HELIX 24 24 TYR B 165 LYS B 169 5 5 HELIX 25 25 ILE B 182 ARG B 193 1 12 HELIX 26 26 PRO B 211 ASP B 227 1 17 HELIX 27 27 ARG B 243 HIS B 257 1 15 HELIX 28 28 ASN B 270 GLU B 275 5 6 HELIX 29 29 PRO B 288 ASP B 293 1 6 HELIX 30 30 THR B 304 LEU B 312 1 9 SHEET 1 A 9 SER A 337 HIS A 339 0 SHEET 2 A 9 THR A 90 PRO A 94 -1 N THR A 90 O HIS A 339 SHEET 3 A 9 ALA A 73 GLY A 78 1 N HIS A 76 O ILE A 91 SHEET 4 A 9 ARG A 21 GLN A 25 1 N LEU A 23 O ILE A 75 SHEET 5 A 9 GLU A 47 HIS A 51 1 O HIS A 51 N ILE A 24 SHEET 6 A 9 GLU B 260 MET B 266 1 O VAL B 265 N LEU A 50 SHEET 7 A 9 LYS B 230 SER B 236 1 N VAL B 233 O ARG B 262 SHEET 8 A 9 ALA B 281 VAL B 284 1 O VAL B 283 N ILE B 234 SHEET 9 A 9 VAL B 302 LEU B 303 1 O LEU B 303 N VAL B 284 SHEET 1 B 5 GLU A 144 SER A 146 0 SHEET 2 B 5 LYS A 118 THR A 123 1 N ILE A 119 O SER A 146 SHEET 3 B 5 GLY A 174 ILE A 178 1 O LEU A 176 N ILE A 120 SHEET 4 B 5 LYS A 195 ILE A 199 1 O LEU A 197 N PHE A 177 SHEET 5 B 5 PHE A 206 TRP A 208 -1 O SER A 207 N ALA A 198 SHEET 1 C 9 VAL A 302 LEU A 303 0 SHEET 2 C 9 ALA A 281 VAL A 284 1 N VAL A 284 O LEU A 303 SHEET 3 C 9 LYS A 230 SER A 236 1 N ILE A 234 O VAL A 283 SHEET 4 C 9 GLU A 260 MET A 266 1 O ILE A 264 N VAL A 233 SHEET 5 C 9 GLU B 47 HIS B 51 1 O LEU B 50 N VAL A 265 SHEET 6 C 9 ARG B 21 GLN B 25 1 N ILE B 24 O HIS B 51 SHEET 7 C 9 ALA B 73 GLY B 78 1 O ILE B 75 N LEU B 23 SHEET 8 C 9 THR B 90 PRO B 94 1 O ILE B 91 N LEU B 74 SHEET 9 C 9 SER B 337 HIS B 339 -1 O HIS B 339 N THR B 90 SHEET 1 D 5 GLU B 144 SER B 146 0 SHEET 2 D 5 LYS B 118 THR B 123 1 N ILE B 119 O SER B 146 SHEET 3 D 5 GLY B 174 ILE B 178 1 O LEU B 176 N ILE B 120 SHEET 4 D 5 VAL B 196 ILE B 199 1 O LEU B 197 N PHE B 177 SHEET 5 D 5 PHE B 206 TRP B 208 -1 O SER B 207 N ALA B 198 LINK SG CYS A 59 FE4 SF4 A 343 1555 1555 2.37 LINK SG CYS A 163 FE3 SF4 A 343 1555 1555 2.35 LINK SG CYS A 287 FE1 SF4 A 343 1555 1555 2.33 LINK SG CYS B 59 FE4 SF4 B 343 1555 1555 2.35 LINK SG CYS B 163 FE3 SF4 B 343 1555 1555 2.33 LINK SG CYS B 287 FE1 SF4 B 343 1555 1555 2.33 SITE 1 AC1 5 CYS A 59 ARG A 153 CYS A 163 CYS A 287 SITE 2 AC1 5 SO4 A 344 SITE 1 AC2 5 LEU A 161 GLY A 162 HIS A 184 ARG A 289 SITE 2 AC2 5 SF4 A 343 SITE 1 AC3 5 TYR B 56 CYS B 59 CYS B 163 CYS B 287 SITE 2 AC3 5 SO4 B 344 SITE 1 AC4 6 LEU B 161 GLY B 162 HIS B 184 ARG B 289 SITE 2 AC4 6 SF4 B 343 HOH B 408 SITE 1 AC5 5 ARG A 32 GLY B 148 ARG B 149 HOH B 440 SITE 2 AC5 5 HOH B 444 CRYST1 55.695 80.525 162.142 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 0.017955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006167 0.00000