HEADER BIOSYNTHETIC PROTEIN 19-FEB-09 3GBF TITLE PHPD WITH CADMIUM COMPLEXED WITH HYDROETHYLPHOSPHONATE (HEP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHPD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VIRIDOCHROMOGENES; SOURCE 3 ORGANISM_TAXID: 1938; SOURCE 4 GENE: PHPD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15 KEYWDS ANTIBIOTIC BIOSYNTHESIS, IRON DEPENDENT OXYGENASE, BIOSYNTHETIC KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,S.K.NAIR REVDAT 2 30-OCT-24 3GBF 1 REMARK LINK REVDAT 1 09-JUN-09 3GBF 0 JRNL AUTH R.M.CICCHILLIO,H.ZHANG,J.A.V.BLODGETT,J.T.WHITTECK,G.LI, JRNL AUTH 2 S.K.NAIR,W.A.VAN DER DONK,W.W.METCALF JRNL TITL AN UNUSUAL CARBON-CARBON BOND CLEAVAGE REACTION IN THE JRNL TITL 2 BIOSYNTHESIS OF THE HERBICIDE PHOSPHINOTHRICIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 29741 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1587 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1958 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3165 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.48000 REMARK 3 B22 (A**2) : 3.55000 REMARK 3 B33 (A**2) : -1.07000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.193 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.172 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.168 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3249 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4435 ; 1.225 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 411 ; 6.274 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 145 ;33.648 ;22.759 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 475 ;15.620 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;18.165 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 493 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2521 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1455 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2217 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 263 ; 0.132 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.213 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 133 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.128 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2105 ; 0.710 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3293 ; 1.103 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1302 ; 1.844 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1142 ; 2.718 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3GBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000051656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 28.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29000 REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M SODIUM ACETATE, 100 MM HEPES PH REMARK 280 7.5, 50 MM CADMIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.79750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.79750 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 42.48700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.34750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.48700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.34750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 50.79750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.48700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.34750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 50.79750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.48700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.34750 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -225.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 84.97400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.79750 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 38 REMARK 465 ASP A 39 REMARK 465 GLU A 40 REMARK 465 ALA A 41 REMARK 465 ASN A 42 REMARK 465 GLU A 43 REMARK 465 PRO A 44 REMARK 465 ASP A 45 REMARK 465 HIS A 297 REMARK 465 ASP A 298 REMARK 465 GLY A 299 REMARK 465 ASP A 342 REMARK 465 ALA A 343 REMARK 465 ASP A 344 REMARK 465 GLY A 345 REMARK 465 ARG A 346 REMARK 465 GLY A 347 REMARK 465 ALA A 348 REMARK 465 ARG A 434 REMARK 465 ASP A 435 REMARK 465 LEU A 436 REMARK 465 ALA A 437 REMARK 465 GLY A 438 REMARK 465 TRP A 439 REMARK 465 GLY A 440 REMARK 465 TYR A 441 REMARK 465 ASP A 442 REMARK 465 ASN A 443 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 ARG A 2 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 35 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 46 CG CD REMARK 470 HIS A 68 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 69 CG CD NE CZ NH1 NH2 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 ND1 HIS A 330 CD CD A 512 1.82 REMARK 500 O HOH A 531 O HOH A 719 2.07 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 THR A 72 -61.01 -121.08 REMARK 500 TYR A 179 -20.48 81.16 REMARK 500 ASP A 383 -19.80 83.82 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 CD A 507 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 10 ND1 REMARK 620 2 HOH A 481 O 72.5 REMARK 620 3 HOH A 561 O 138.1 96.9 REMARK 620 4 HOH A 704 O 92.2 155.2 81.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 509 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD2 REMARK 620 2 HOH A 519 O 119.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 510 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 75 NE2 REMARK 620 2 HOH A 698 O 91.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 504 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 80 OE1 REMARK 620 2 GLU A 80 OE2 53.1 REMARK 620 3 HOH A 531 O 86.6 135.7 REMARK 620 4 HOH A 707 O 91.5 99.7 59.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 513 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 129 NE2 REMARK 620 2 GLU A 176 OE1 95.2 REMARK 620 3 HIS A 182 NE2 90.5 78.9 REMARK 620 4 2HE A 550 O2 98.1 165.3 94.8 REMARK 620 5 2HE A 550 O4 174.4 85.6 95.0 81.7 REMARK 620 6 HOH A 725 O 89.1 91.3 170.1 95.1 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 508 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 142 OD1 REMARK 620 2 ASP A 142 OD2 54.2 REMARK 620 3 HIS A 160 ND1 92.5 87.8 REMARK 620 4 HIS A 163 NE2 76.5 97.7 161.1 REMARK 620 5 HOH A 451 O 152.2 98.5 91.2 105.8 REMARK 620 6 HOH A 464 O 100.2 152.8 84.5 82.5 107.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 505 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 309 OD1 REMARK 620 2 ASP A 309 OD2 55.0 REMARK 620 3 HOH A 496 O 133.3 78.9 REMARK 620 4 HOH A 705 O 94.6 101.1 86.2 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 2HE A 550 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 513 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G7D RELATED DB: PDB REMARK 900 NATIVE PHPD WITH CADMIUM ATOMS DBREF 3GBF A 1 443 UNP Q5IW40 Q5IW40_STRVR 1 443 SEQRES 1 A 443 MSE ARG ILE ASP PRO PHE LYS LEU ALA HIS TRP MSE ASN SEQRES 2 A 443 ALA ARG LYS TYR THR ALA ALA GLN THR ALA ASP LEU ALA SEQRES 3 A 443 GLY LEU PRO LEU ASP ASP LEU ARG ARG LEU LEU GLY ASP SEQRES 4 A 443 GLU ALA ASN GLU PRO ASP PRO ALA ALA ALA THR ALA LEU SEQRES 5 A 443 ALA GLU ALA LEU SER VAL GLU PRO SER GLN LEU ALA ALA SEQRES 6 A 443 ASP ALA HIS ARG ASN LEU THR VAL VAL HIS LYS SER ALA SEQRES 7 A 443 GLU GLU MSE HIS ALA SER ARG ARG PRO ILE GLN ARG ASP SEQRES 8 A 443 GLY ILE HIS PHE TYR ASN TYR TYR THR LEU ALA ALA PRO SEQRES 9 A 443 GLU GLY ARG VAL ALA PRO VAL VAL LEU ASP ILE LEU CYS SEQRES 10 A 443 PRO SER ASP ARG LEU PRO ALA LEU ASN ASN GLY HIS LEU SEQRES 11 A 443 GLU PRO ALA ILE THR VAL ASN LEU GLY PRO GLY ASP ILE SEQRES 12 A 443 ASN GLY ARG TRP GLY GLU GLU ILE THR PRO GLN THR TRP SEQRES 13 A 443 ARG VAL LEU HIS ALA ASN HIS GLY GLY ASP ARG TRP ILE SEQRES 14 A 443 THR GLY ASP SER TYR VAL GLU PRO SER TYR CYS PRO HIS SEQRES 15 A 443 SER TYR SER LEU ALA GLY ASP ALA PRO ALA ARG ILE VAL SEQRES 16 A 443 SER TYR THR ALA GLN SER ASN ILE SER PRO LEU MSE THR SEQRES 17 A 443 GLU ALA ASN ASN TRP SER THR GLY ALA PHE GLU GLU ALA SEQRES 18 A 443 LEU LYS ALA LEU SER GLY LYS VAL SER ALA GLY SER VAL SEQRES 19 A 443 LEU ASP LEU PHE LEU ALA ARG ARG ALA HIS THR ARG THR SEQRES 20 A 443 SER ALA ALA GLU ALA ALA GLY VAL PRO PRO ALA ASP LEU SEQRES 21 A 443 GLU ALA ALA LEU ARG SER PRO ALA SER GLU THR GLY LEU SEQRES 22 A 443 THR VAL LEU ARG THR LEU GLY ARG ALA LEU GLY PHE ASP SEQRES 23 A 443 TYR ARG VAL LEU LEU PRO ALA ASP ASP GLN HIS ASP GLY SEQRES 24 A 443 VAL GLY LYS THR TRP THR THR ILE GLU ASP SER ARG ARG SEQRES 25 A 443 SER ARG ARG THR PHE GLY THR TYR GLU ALA ALA SER MSE SEQRES 26 A 443 ALA SER ALA ALA HIS LEU PRO ASP LEU VAL GLY SER PHE SEQRES 27 A 443 LEU ARG VAL ASP ALA ASP GLY ARG GLY ALA ASP LEU ILE SEQRES 28 A 443 ASP HIS ALA GLU ASN HIS TYR VAL VAL THR GLU GLY ARG SEQRES 29 A 443 LEU THR LEU GLU TRP ASP GLY PRO ASP GLY PRO ALA SER SEQRES 30 A 443 VAL GLU LEU GLU PRO ASP GLY SER ALA TRP THR GLY PRO SEQRES 31 A 443 PHE VAL ARG HIS ARG TRP HIS GLY THR GLY THR VAL LEU SEQRES 32 A 443 LYS PHE GLY SER GLY ALA HIS LEU GLY TYR GLN ASP TRP SEQRES 33 A 443 LEU GLU LEU THR ASN THR PHE GLU PRO ALA ALA THR LEU SEQRES 34 A 443 ARG ARG GLY ARG ARG ASP LEU ALA GLY TRP GLY TYR ASP SEQRES 35 A 443 ASN MODRES 3GBF MSE A 1 MET SELENOMETHIONINE MODRES 3GBF MSE A 12 MET SELENOMETHIONINE MODRES 3GBF MSE A 81 MET SELENOMETHIONINE MODRES 3GBF MSE A 207 MET SELENOMETHIONINE MODRES 3GBF MSE A 325 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 12 8 HET MSE A 81 8 HET MSE A 207 8 HET MSE A 325 8 HET 2HE A 550 7 HET CD A 501 1 HET CD A 502 1 HET CD A 503 1 HET CD A 504 1 HET CD A 505 1 HET CD A 506 1 HET CD A 507 1 HET CD A 508 1 HET CD A 509 1 HET CD A 510 1 HET CD A 511 1 HET CD A 512 1 HET CD A 513 1 HETNAM MSE SELENOMETHIONINE HETNAM 2HE (2-HYDROXYETHYL)PHOSPHONIC ACID HETNAM CD CADMIUM ION FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 2HE C2 H7 O4 P FORMUL 3 CD 13(CD 2+) FORMUL 16 HOH *268(H2 O) HELIX 1 1 ASP A 4 LYS A 16 1 13 HELIX 2 2 THR A 18 GLY A 27 1 10 HELIX 3 3 PRO A 29 LEU A 37 1 9 HELIX 4 4 PRO A 46 LEU A 56 1 11 HELIX 5 5 GLU A 59 LEU A 63 5 5 HELIX 6 6 SER A 77 SER A 84 1 8 HELIX 7 7 ILE A 203 ASN A 211 1 9 HELIX 8 8 SER A 214 SER A 226 1 13 HELIX 9 9 SER A 230 ARG A 242 1 13 HELIX 10 10 THR A 245 GLY A 254 1 10 HELIX 11 11 PRO A 256 SER A 266 1 11 HELIX 12 12 SER A 269 GLY A 284 1 16 HELIX 13 13 ASP A 286 LEU A 291 5 6 HELIX 14 14 THR A 306 SER A 313 1 8 HELIX 15 15 GLY A 412 ASN A 421 1 10 HELIX 16 16 GLU A 424 ARG A 433 1 10 SHEET 1 A 7 VAL A 73 LYS A 76 0 SHEET 2 A 7 SER A 385 THR A 388 -1 O SER A 385 N LYS A 76 SHEET 3 A 7 GLU A 355 GLU A 362 -1 N TYR A 358 O ALA A 386 SHEET 4 A 7 GLY A 400 SER A 407 -1 O LEU A 403 N VAL A 359 SHEET 5 A 7 VAL A 335 VAL A 341 -1 N SER A 337 O LYS A 404 SHEET 6 A 7 TYR A 320 SER A 324 -1 N ALA A 323 O PHE A 338 SHEET 7 A 7 ARG A 315 PHE A 317 -1 N PHE A 317 O TYR A 320 SHEET 1 B 6 ARG A 86 ARG A 90 0 SHEET 2 B 6 ILE A 93 THR A 100 -1 O TYR A 98 N ARG A 86 SHEET 3 B 6 VAL A 111 ILE A 115 -1 O VAL A 112 N TYR A 99 SHEET 4 B 6 ALA A 192 THR A 198 -1 O ALA A 192 N ILE A 115 SHEET 5 B 6 ALA A 133 PRO A 140 -1 N ILE A 134 O TYR A 197 SHEET 6 B 6 SER A 173 GLU A 176 -1 O GLU A 176 N ALA A 133 SHEET 1 C 3 TRP A 156 LEU A 159 0 SHEET 2 C 3 ILE A 143 ARG A 146 -1 N GLY A 145 O ARG A 157 SHEET 3 C 3 SER A 183 LEU A 186 -1 O SER A 185 N ASN A 144 SHEET 1 D 3 GLY A 374 LEU A 380 0 SHEET 2 D 3 LEU A 365 GLY A 371 -1 N TRP A 369 O ALA A 376 SHEET 3 D 3 HIS A 394 HIS A 397 -1 O ARG A 395 N GLU A 368 LINK C MSE A 1 N ARG A 2 1555 1555 1.33 LINK C TRP A 11 N MSE A 12 1555 1555 1.33 LINK C MSE A 12 N ASN A 13 1555 1555 1.33 LINK C GLU A 80 N MSE A 81 1555 1555 1.33 LINK C MSE A 81 N HIS A 82 1555 1555 1.34 LINK C LEU A 206 N MSE A 207 1555 1555 1.33 LINK C MSE A 207 N THR A 208 1555 1555 1.33 LINK C SER A 324 N MSE A 325 1555 1555 1.34 LINK C MSE A 325 N ALA A 326 1555 1555 1.33 LINK ND1 HIS A 10 CD CD A 507 1555 1555 2.43 LINK OD2 ASP A 66 CD CD A 509 1555 1555 2.60 LINK NE2 HIS A 75 CD CD A 510 1555 1555 2.44 LINK OE1 GLU A 80 CD CD A 504 1555 1555 2.46 LINK OE2 GLU A 80 CD CD A 504 1555 1555 2.43 LINK ND1 HIS A 94 CD CD A 506 1555 1555 2.42 LINK NE2 HIS A 129 CD CD A 513 1555 1555 2.27 LINK OD1 ASP A 142 CD CD A 508 1555 1555 2.59 LINK OD2 ASP A 142 CD CD A 508 1555 1555 2.13 LINK ND1 HIS A 160 CD CD A 508 1555 1555 2.30 LINK NE2 HIS A 163 CD CD A 508 1555 1555 2.48 LINK OE1 GLU A 176 CD CD A 513 1555 1555 2.34 LINK NE2 HIS A 182 CD CD A 513 1555 1555 2.30 LINK OD2 ASP A 189 CD CD A 503 1555 1555 2.37 LINK OD1 ASP A 294 CD CD A 512 1555 1555 2.43 LINK OD1 ASP A 309 CD CD A 505 1555 1555 2.48 LINK OD2 ASP A 309 CD CD A 505 1555 1555 2.25 LINK O HOH A 451 CD CD A 508 1555 1555 2.41 LINK O HOH A 464 CD CD A 508 1555 1555 2.55 LINK O HOH A 481 CD CD A 507 1555 1555 2.28 LINK O HOH A 496 CD CD A 505 1555 1555 2.23 LINK CD CD A 504 O HOH A 531 1555 1555 2.28 LINK CD CD A 504 O HOH A 707 1555 1555 2.31 LINK CD CD A 505 O HOH A 705 1555 1555 2.13 LINK CD CD A 507 O HOH A 561 1555 1555 2.49 LINK CD CD A 507 O HOH A 704 1555 1555 2.14 LINK CD CD A 509 O HOH A 519 1555 1555 2.57 LINK CD CD A 510 O HOH A 698 1555 1555 2.21 LINK CD CD A 511 O HOH A 717 1555 1555 2.41 LINK CD CD A 513 O2 2HE A 550 1555 1555 2.52 LINK CD CD A 513 O4 2HE A 550 1555 1555 2.02 LINK CD CD A 513 O HOH A 725 1555 1555 2.33 CISPEP 1 GLY A 139 PRO A 140 0 5.20 CISPEP 2 THR A 399 GLY A 400 0 -22.48 CISPEP 3 HIS A 410 LEU A 411 0 -1.56 SITE 1 AC1 12 LYS A 16 ARG A 90 TYR A 98 ASN A 126 SITE 2 AC1 12 HIS A 129 GLU A 176 HIS A 182 SER A 196 SITE 3 AC1 12 HOH A 500 CD A 513 HOH A 720 HOH A 725 SITE 1 AC2 2 CYS A 180 CD A 502 SITE 1 AC3 3 CYS A 180 CD A 501 HOH A 672 SITE 1 AC4 3 ASP A 189 GLU A 368 HIS A 397 SITE 1 AC5 3 GLU A 80 HOH A 531 HOH A 707 SITE 1 AC6 5 ASP A 32 ASP A 309 HOH A 496 HOH A 528 SITE 2 AC6 5 HOH A 705 SITE 1 AC7 1 HIS A 94 SITE 1 AC8 5 HIS A 10 GLU A 131 HOH A 481 HOH A 561 SITE 2 AC8 5 HOH A 704 SITE 1 AC9 5 ASP A 142 HIS A 160 HIS A 163 HOH A 451 SITE 2 AC9 5 HOH A 464 SITE 1 BC1 2 ASP A 66 HOH A 519 SITE 1 BC2 2 HIS A 75 HOH A 698 SITE 1 BC3 3 HIS A 410 HOH A 641 HOH A 717 SITE 1 BC4 3 ASP A 294 LYS A 302 HIS A 330 SITE 1 BC5 5 HIS A 129 GLU A 176 HIS A 182 2HE A 550 SITE 2 BC5 5 HOH A 725 CRYST1 84.974 94.695 101.595 90.00 90.00 90.00 C 2 2 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 0.011768 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009843 0.00000 HETATM 1 N MSE A 1 44.592 47.109 34.833 1.00 55.34 N HETATM 2 CA MSE A 1 45.218 47.082 33.476 1.00 55.97 C HETATM 3 C MSE A 1 46.721 46.767 33.565 1.00 53.43 C HETATM 4 O MSE A 1 47.554 47.471 32.990 1.00 53.61 O HETATM 5 CB MSE A 1 44.966 48.411 32.737 1.00 55.80 C HETATM 6 CG MSE A 1 43.480 48.762 32.501 1.00 57.77 C HETATM 7 SE MSE A 1 42.823 50.388 33.422 1.00 62.42 SE HETATM 8 CE MSE A 1 43.443 51.739 32.143 1.00 60.35 C