HEADER OXIDOREDUCTASE 21-FEB-14 3WRA TITLE CRYSTAL STRUCTURE OF THE DESB-GALLATE COMPLEX EXPOSED TO AEROBIC TITLE 2 ATOMOSPHERE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALLATE DIOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DESB, TYPE II EXTRADIOL DIOXYGENASE; COMPND 5 EC: 1.13.11.58; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPHINGOMONAS PAUCIMOBILIS; SOURCE 3 ORGANISM_TAXID: 13689; SOURCE 4 STRAIN: SYK-6; SOURCE 5 GENE: DESB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PEVK3G KEYWDS OXIDOREDUCTASE, EXTRADIOL DIOXYGENASE, FE2+ BINDING, DOMAIN-SWAP KEYWDS 2 DIMER EXPDTA X-RAY DIFFRACTION AUTHOR K.SUGIMOTO,M.SENDA,D.KASAI,M.FUKUDA,E.MASAI,T.SENDA REVDAT 3 03-APR-24 3WRA 1 REMARK REVDAT 2 20-MAR-24 3WRA 1 REMARK LINK REVDAT 1 30-APR-14 3WRA 0 JRNL AUTH K.SUGIMOTO,M.SENDA,D.KASAI,M.FUKUDA,E.MASAI,T.SENDA JRNL TITL MOLECULAR MECHANISM OF STRICT SUBSTRATE SPECIFICITY OF AN JRNL TITL 2 EXTRADIOL DIOXYGENASE, DESB, DERIVED FROM SPHINGOBIUM SP. JRNL TITL 3 SYK-6 JRNL REF PLOS ONE V. 9 92249 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24657997 JRNL DOI 10.1371/JOURNAL.PONE.0092249 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 46934 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2471 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3420 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6447 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : -2.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.163 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.148 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6637 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9003 ; 1.368 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 810 ; 5.857 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 328 ;35.922 ;23.476 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1052 ;15.008 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;17.740 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 930 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5213 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 4038 ; 0.621 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6470 ; 1.138 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2599 ; 1.895 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2533 ; 3.002 ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3WRA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000096693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49264 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 56.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.470 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5200 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) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.59 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.710 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: DESB SUBSTRATE-FREE FORM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG8000, 0.1M SODIUM ACETATE, 0.1M REMARK 280 HEPES-NAOH, PH 7.75, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 32.42850 REMARK 290 SMTRY3 2 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: 9040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 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 1 REMARK 465 ILE A 410 REMARK 465 THR A 411 REMARK 465 TYR A 412 REMARK 465 SER A 413 REMARK 465 VAL A 414 REMARK 465 ALA A 415 REMARK 465 GLY A 416 REMARK 465 LYS A 417 REMARK 465 GLN A 418 REMARK 465 MET B 1 REMARK 465 ARG B 406 REMARK 465 ASN B 407 REMARK 465 ALA B 408 REMARK 465 ALA B 409 REMARK 465 ILE B 410 REMARK 465 THR B 411 REMARK 465 TYR B 412 REMARK 465 SER B 413 REMARK 465 VAL B 414 REMARK 465 ALA B 415 REMARK 465 GLY B 416 REMARK 465 LYS B 417 REMARK 465 GLN B 418 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 24 32.65 -77.06 REMARK 500 ASP A 27 137.30 -32.13 REMARK 500 HIS A 59 59.50 -99.44 REMARK 500 THR A 61 -72.42 -113.26 REMARK 500 PHE A 64 -75.29 -143.92 REMARK 500 HIS A 136 39.36 -148.44 REMARK 500 PRO A 177 31.05 -79.07 REMARK 500 LEU A 190 -126.74 -100.75 REMARK 500 HIS A 258 136.94 -171.75 REMARK 500 SER A 265 -126.75 -149.62 REMARK 500 ASP A 340 58.93 -141.29 REMARK 500 ASN B 23 73.90 62.06 REMARK 500 HIS B 59 61.71 -107.54 REMARK 500 THR B 61 -72.49 -116.33 REMARK 500 PHE B 64 -71.16 -151.31 REMARK 500 HIS B 136 15.56 -154.24 REMARK 500 PRO B 177 53.87 -69.54 REMARK 500 LEU B 190 -118.72 -89.09 REMARK 500 ASP B 217 58.13 -155.56 REMARK 500 GLU B 239 -8.31 -56.95 REMARK 500 SER B 265 -112.17 -135.51 REMARK 500 ASP B 340 50.39 -152.25 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 FE2 A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 ASN A 57 OD1 91.2 REMARK 620 3 HIS A 59 NE2 96.4 100.1 REMARK 620 4 GLU A 239 OE1 98.2 78.6 165.4 REMARK 620 5 HOH A 621 O 88.4 170.6 89.3 92.1 REMARK 620 6 HOH A 625 O 170.6 96.3 87.9 77.9 83.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 12 NE2 REMARK 620 2 ASN B 57 OD1 87.2 REMARK 620 3 HIS B 59 NE2 100.1 96.3 REMARK 620 4 GLU B 239 OE1 97.5 84.8 162.4 REMARK 620 5 HOH B 604 O 90.1 171.9 91.7 88.0 REMARK 620 6 HOH B 610 O 170.1 102.0 82.7 80.0 80.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WKU RELATED DB: PDB REMARK 900 RELATED ID: 3WPM RELATED DB: PDB REMARK 900 RELATED ID: 3WR3 RELATED DB: PDB REMARK 900 RELATED ID: 3WR4 RELATED DB: PDB REMARK 900 RELATED ID: 3WR8 RELATED DB: PDB REMARK 900 RELATED ID: 3WR9 RELATED DB: PDB REMARK 900 RELATED ID: 3WRB RELATED DB: PDB REMARK 900 RELATED ID: 3WRC RELATED DB: PDB DBREF 3WRA A 1 418 UNP Q5NTE5 Q5NTE5_SPHPI 1 418 DBREF 3WRA B 1 418 UNP Q5NTE5 Q5NTE5_SPHPI 1 418 SEQRES 1 A 418 MET ALA LYS ILE ILE GLY GLY PHE ALA VAL SER HIS THR SEQRES 2 A 418 PRO THR ILE ALA PHE ALA HIS ASP ALA ASN LYS TYR ASP SEQRES 3 A 418 ASP PRO VAL TRP ALA PRO ILE PHE GLN GLY PHE GLU PRO SEQRES 4 A 418 VAL LYS GLN TRP LEU ALA GLU GLN LYS PRO ASP VAL THR SEQRES 5 A 418 PHE TYR VAL TYR ASN ASP HIS MET THR SER PHE PHE GLU SEQRES 6 A 418 HIS TYR SER HIS PHE ALA LEU GLY VAL GLY GLU GLU TYR SEQRES 7 A 418 SER PRO ALA ASP GLU GLY GLY GLY GLN ARG ASP LEU PRO SEQRES 8 A 418 PRO ILE LYS GLY ASP PRO GLU LEU ALA LYS HIS ILE ALA SEQRES 9 A 418 GLU CYS LEU VAL ALA ASP GLU PHE ASP LEU ALA TYR TRP SEQRES 10 A 418 GLN GLY MET GLY LEU ASP HIS GLY ALA PHE SER PRO LEU SEQRES 11 A 418 SER VAL LEU LEU PRO HIS GLU HIS GLY TRP PRO CYS ARG SEQRES 12 A 418 ILE VAL PRO LEU GLN CYS GLY VAL LEU GLN HIS PRO ILE SEQRES 13 A 418 PRO LYS ALA ARG ARG PHE TRP ASN PHE GLY ARG SER LEU SEQRES 14 A 418 ARG ARG ALA ILE GLN SER TYR PRO ARG ASP ILE LYS VAL SEQRES 15 A 418 ALA ILE ALA GLY THR GLY GLY LEU SER HIS GLN VAL HIS SEQRES 16 A 418 GLY GLU ARG ALA GLY PHE ASN ASN THR GLU TRP ASP MET SEQRES 17 A 418 GLU PHE MET GLU ARG LEU ALA ASN ASP PRO GLU SER LEU SEQRES 18 A 418 LEU GLY ALA THR VAL THR ASP LEU ALA LYS LYS GLY GLY SEQRES 19 A 418 TRP GLU GLY ALA GLU VAL VAL MET TRP LEU LEU MET ARG SEQRES 20 A 418 GLY ALA LEU SER PRO GLU VAL LYS THR LEU HIS GLN SER SEQRES 21 A 418 TYR PHE LEU PRO SER MET THR ALA ILE ALA THR MET LEU SEQRES 22 A 418 PHE GLU ASP GLN GLY ASP ALA ALA PRO PRO ALA GLU SER SEQRES 23 A 418 ASP GLU ALA LEU ARG ALA ARG ALA LYS ARG GLU LEU ALA SEQRES 24 A 418 GLY VAL GLU GLU ILE GLU GLY THR TYR PRO PHE THR ILE SEQRES 25 A 418 ASP ARG ALA VAL LYS GLY PHE ARG ILE ASN HIS PHE LEU SEQRES 26 A 418 HIS ARG LEU ILE GLU PRO ASP PHE ARG LYS ARG PHE VAL SEQRES 27 A 418 GLU ASP PRO GLU GLY LEU PHE ALA GLU SER ASP LEU THR SEQRES 28 A 418 GLU GLU GLU LYS SER LEU ILE ARG ASN ARG ASP TRP ILE SEQRES 29 A 418 GLY MET ILE HIS TYR GLY VAL ILE PHE PHE MET LEU GLU SEQRES 30 A 418 LYS MET ALA ALA VAL LEU GLY ILE GLY ASN ILE ASP VAL SEQRES 31 A 418 TYR ALA ALA PHE ARG GLY LEU SER VAL PRO GLU PHE GLN SEQRES 32 A 418 LYS THR ARG ASN ALA ALA ILE THR TYR SER VAL ALA GLY SEQRES 33 A 418 LYS GLN SEQRES 1 B 418 MET ALA LYS ILE ILE GLY GLY PHE ALA VAL SER HIS THR SEQRES 2 B 418 PRO THR ILE ALA PHE ALA HIS ASP ALA ASN LYS TYR ASP SEQRES 3 B 418 ASP PRO VAL TRP ALA PRO ILE PHE GLN GLY PHE GLU PRO SEQRES 4 B 418 VAL LYS GLN TRP LEU ALA GLU GLN LYS PRO ASP VAL THR SEQRES 5 B 418 PHE TYR VAL TYR ASN ASP HIS MET THR SER PHE PHE GLU SEQRES 6 B 418 HIS TYR SER HIS PHE ALA LEU GLY VAL GLY GLU GLU TYR SEQRES 7 B 418 SER PRO ALA ASP GLU GLY GLY GLY GLN ARG ASP LEU PRO SEQRES 8 B 418 PRO ILE LYS GLY ASP PRO GLU LEU ALA LYS HIS ILE ALA SEQRES 9 B 418 GLU CYS LEU VAL ALA ASP GLU PHE ASP LEU ALA TYR TRP SEQRES 10 B 418 GLN GLY MET GLY LEU ASP HIS GLY ALA PHE SER PRO LEU SEQRES 11 B 418 SER VAL LEU LEU PRO HIS GLU HIS GLY TRP PRO CYS ARG SEQRES 12 B 418 ILE VAL PRO LEU GLN CYS GLY VAL LEU GLN HIS PRO ILE SEQRES 13 B 418 PRO LYS ALA ARG ARG PHE TRP ASN PHE GLY ARG SER LEU SEQRES 14 B 418 ARG ARG ALA ILE GLN SER TYR PRO ARG ASP ILE LYS VAL SEQRES 15 B 418 ALA ILE ALA GLY THR GLY GLY LEU SER HIS GLN VAL HIS SEQRES 16 B 418 GLY GLU ARG ALA GLY PHE ASN ASN THR GLU TRP ASP MET SEQRES 17 B 418 GLU PHE MET GLU ARG LEU ALA ASN ASP PRO GLU SER LEU SEQRES 18 B 418 LEU GLY ALA THR VAL THR ASP LEU ALA LYS LYS GLY GLY SEQRES 19 B 418 TRP GLU GLY ALA GLU VAL VAL MET TRP LEU LEU MET ARG SEQRES 20 B 418 GLY ALA LEU SER PRO GLU VAL LYS THR LEU HIS GLN SER SEQRES 21 B 418 TYR PHE LEU PRO SER MET THR ALA ILE ALA THR MET LEU SEQRES 22 B 418 PHE GLU ASP GLN GLY ASP ALA ALA PRO PRO ALA GLU SER SEQRES 23 B 418 ASP GLU ALA LEU ARG ALA ARG ALA LYS ARG GLU LEU ALA SEQRES 24 B 418 GLY VAL GLU GLU ILE GLU GLY THR TYR PRO PHE THR ILE SEQRES 25 B 418 ASP ARG ALA VAL LYS GLY PHE ARG ILE ASN HIS PHE LEU SEQRES 26 B 418 HIS ARG LEU ILE GLU PRO ASP PHE ARG LYS ARG PHE VAL SEQRES 27 B 418 GLU ASP PRO GLU GLY LEU PHE ALA GLU SER ASP LEU THR SEQRES 28 B 418 GLU GLU GLU LYS SER LEU ILE ARG ASN ARG ASP TRP ILE SEQRES 29 B 418 GLY MET ILE HIS TYR GLY VAL ILE PHE PHE MET LEU GLU SEQRES 30 B 418 LYS MET ALA ALA VAL LEU GLY ILE GLY ASN ILE ASP VAL SEQRES 31 B 418 TYR ALA ALA PHE ARG GLY LEU SER VAL PRO GLU PHE GLN SEQRES 32 B 418 LYS THR ARG ASN ALA ALA ILE THR TYR SER VAL ALA GLY SEQRES 33 B 418 LYS GLN HET FE2 A 501 1 HET FE2 B 501 1 HETNAM FE2 FE (II) ION FORMUL 3 FE2 2(FE 2+) FORMUL 5 HOH *200(H2 O) HELIX 1 1 THR A 13 ALA A 22 1 10 HELIX 2 2 TRP A 30 GLY A 36 1 7 HELIX 3 3 PHE A 37 LYS A 48 1 12 HELIX 4 4 ASP A 96 ASP A 110 1 15 HELIX 5 5 ASP A 123 LEU A 134 1 12 HELIX 6 6 LYS A 158 TYR A 176 1 19 HELIX 7 7 ASN A 203 ASP A 217 1 15 HELIX 8 8 PRO A 218 LEU A 222 5 5 HELIX 9 9 THR A 225 GLY A 234 1 10 HELIX 10 10 TRP A 235 GLU A 239 5 5 HELIX 11 11 VAL A 240 ALA A 249 1 10 HELIX 12 12 SER A 286 LYS A 295 1 10 HELIX 13 13 GLY A 300 ILE A 304 5 5 HELIX 14 14 THR A 311 GLY A 318 1 8 HELIX 15 15 GLY A 318 ARG A 327 1 10 HELIX 16 16 GLU A 330 ASP A 340 1 11 HELIX 17 17 ASP A 340 SER A 348 1 9 HELIX 18 18 THR A 351 ASN A 360 1 10 HELIX 19 19 ASP A 362 GLY A 370 1 9 HELIX 20 20 ILE A 372 LEU A 383 1 12 HELIX 21 21 GLY A 386 GLY A 396 1 11 HELIX 22 22 SER A 398 THR A 405 1 8 HELIX 23 23 THR B 13 ALA B 22 1 10 HELIX 24 24 VAL B 29 LYS B 48 1 20 HELIX 25 25 ASP B 96 ASP B 110 1 15 HELIX 26 26 ASP B 123 LEU B 134 1 12 HELIX 27 27 LYS B 158 SER B 175 1 18 HELIX 28 28 ASN B 203 ASP B 217 1 15 HELIX 29 29 PRO B 218 LEU B 222 5 5 HELIX 30 30 THR B 225 GLY B 234 1 10 HELIX 31 31 TRP B 235 GLU B 239 5 5 HELIX 32 32 VAL B 240 ALA B 249 1 10 HELIX 33 33 SER B 286 ARG B 296 1 11 HELIX 34 34 GLY B 300 ILE B 304 5 5 HELIX 35 35 THR B 311 GLY B 318 1 8 HELIX 36 36 GLY B 318 ARG B 327 1 10 HELIX 37 37 GLU B 330 ASP B 340 1 11 HELIX 38 38 ASP B 340 GLU B 347 1 8 HELIX 39 39 THR B 351 ASN B 360 1 10 HELIX 40 40 ASP B 362 GLY B 370 1 9 HELIX 41 41 ILE B 372 GLY B 384 1 13 HELIX 42 42 GLY B 386 GLY B 396 1 11 HELIX 43 43 SER B 398 LYS B 404 1 7 SHEET 1 A 9 LYS A 255 PHE A 262 0 SHEET 2 A 9 ILE A 269 GLU A 275 -1 O ILE A 269 N PHE A 262 SHEET 3 A 9 LYS A 3 VAL A 10 -1 N GLY A 7 O PHE A 274 SHEET 4 A 9 LYS A 181 THR A 187 1 O VAL A 182 N LYS A 3 SHEET 5 A 9 VAL A 51 TYR A 56 1 N PHE A 53 O ALA A 185 SHEET 6 A 9 ARG A 143 CYS A 149 1 O LEU A 147 N TYR A 54 SHEET 7 A 9 PHE A 70 GLY A 73 -1 N ALA A 71 O GLN A 148 SHEET 8 A 9 ALA A 115 TRP A 117 1 O ALA A 115 N LEU A 72 SHEET 9 A 9 HIS B 66 SER B 68 -1 O TYR B 67 N TYR A 116 SHEET 1 B 9 HIS A 66 SER A 68 0 SHEET 2 B 9 ALA B 115 TRP B 117 -1 O TYR B 116 N TYR A 67 SHEET 3 B 9 PHE B 70 GLY B 73 1 N LEU B 72 O ALA B 115 SHEET 4 B 9 ARG B 143 CYS B 149 -1 O GLN B 148 N ALA B 71 SHEET 5 B 9 VAL B 51 TYR B 56 1 N TYR B 54 O VAL B 145 SHEET 6 B 9 LYS B 181 THR B 187 1 O ALA B 185 N VAL B 55 SHEET 7 B 9 LYS B 3 VAL B 10 1 N LYS B 3 O VAL B 182 SHEET 8 B 9 ILE B 269 ASP B 276 -1 O PHE B 274 N GLY B 7 SHEET 9 B 9 VAL B 254 PHE B 262 -1 N PHE B 262 O ILE B 269 SHEET 1 C 2 GLU A 77 TYR A 78 0 SHEET 2 C 2 ILE A 93 LYS A 94 -1 O ILE A 93 N TYR A 78 SHEET 1 D 2 GLU B 77 TYR B 78 0 SHEET 2 D 2 ILE B 93 LYS B 94 -1 O ILE B 93 N TYR B 78 LINK NE2 HIS A 12 FE FE2 A 501 1555 1555 2.37 LINK OD1 ASN A 57 FE FE2 A 501 1555 1555 2.17 LINK NE2 HIS A 59 FE FE2 A 501 1555 1555 2.23 LINK OE1 GLU A 239 FE FE2 A 501 1555 1555 2.15 LINK FE FE2 A 501 O HOH A 621 1555 1555 2.22 LINK FE FE2 A 501 O HOH A 625 1555 1555 2.30 LINK NE2 HIS B 12 FE FE2 B 501 1555 1555 2.25 LINK OD1 ASN B 57 FE FE2 B 501 1555 1555 2.20 LINK NE2 HIS B 59 FE FE2 B 501 1555 1555 2.17 LINK OE1 GLU B 239 FE FE2 B 501 1555 1555 2.11 LINK FE FE2 B 501 O HOH B 604 1555 1555 2.00 LINK FE FE2 B 501 O HOH B 610 1555 1555 2.23 CISPEP 1 HIS A 154 PRO A 155 0 1.69 CISPEP 2 GLY A 189 LEU A 190 0 -1.75 CISPEP 3 HIS B 154 PRO B 155 0 8.94 CISPEP 4 GLY B 189 LEU B 190 0 -5.27 SITE 1 AC1 6 HIS A 12 ASN A 57 HIS A 59 GLU A 239 SITE 2 AC1 6 HOH A 621 HOH A 625 SITE 1 AC2 6 HIS B 12 ASN B 57 HIS B 59 GLU B 239 SITE 2 AC2 6 HOH B 604 HOH B 610 CRYST1 57.372 64.857 117.656 90.00 96.24 90.00 P 1 21 1 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 0.017430 0.000000 0.001907 0.00000 SCALE2 0.000000 0.015419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008550 0.00000