HEADER HEME-BINDING PROTEIN 31-MAY-12 3VTM TITLE STRUCTURE OF HEME TRANSPORT PROTEIN ISDH-NEAT3 FROM S. AUREUS IN TITLE 2 COMPLEX WITH INDIUM-PORPHYRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON-REGULATED SURFACE DETERMINANT PROTEIN H; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: NEAT DOMAIN, UNP RESIDUES 543-655; COMPND 5 SYNONYM: HAPTOGLOBIN RECEPTOR A, STAPHYLOCOCCUS AUREUS SURFACE COMPND 6 PROTEIN I; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: STRAIN MU50 / ATCC 700699; SOURCE 5 GENE: HARA, ISDH, ISDH-NEAT3, SASI, SAV1731; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS INDIUM, METALLOPORPHYRIN, METAL SELECTIVITY, NEAT DOMAIN, HEME KEYWDS 2 BINDING, HEME TRANSPORT, HEMIN, PPIX, CELL WALL, HEME-BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.T.VU,J.M.M.CAAVEIRO,Y.MORIWAKI,K.TSUMOTO REVDAT 4 08-NOV-23 3VTM 1 REMARK REVDAT 3 22-NOV-17 3VTM 1 REMARK REVDAT 2 21-AUG-13 3VTM 1 JRNL REVDAT 1 15-MAY-13 3VTM 0 JRNL AUTH N.T.VU,Y.MORIWAKI,J.M.M.CAAVEIRO,T.TERADA,H.TSUTSUMI, JRNL AUTH 2 I.HAMACHI,K.SHIMIZU,K.TSUMOTO JRNL TITL SELECTIVE BINDING OF ANTIMICROBIAL PORPHYRINS TO THE JRNL TITL 2 HEME-RECEPTOR ISDH-NEAT3 OF STAPHYLOCOCCUS AUREUS JRNL REF PROTEIN SCI. V. 22 942 2013 JRNL REFN ISSN 0961-8368 JRNL PMID 23649633 JRNL DOI 10.1002/PRO.2276 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.MORIWAKI,J.M.CAAVEIRO,Y.TANAKA,H.TSUTSUMI,I.HAMACHI, REMARK 1 AUTH 2 K.TSUMOTO REMARK 1 TITL MOLECULAR BASIS OF RECOGNITION OF ANTIBACTERIAL PORPHYRINS REMARK 1 TITL 2 BY HEME-TRANSPORTER ISDH-NEAT3 OF STAPHYLOCOCCUS AUREUS. REMARK 1 REF BIOCHEMISTRY V. 50 7311 2011 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 21797259 REMARK 1 DOI 10.1021/BI200493H REMARK 1 REFERENCE 2 REMARK 1 AUTH M.WATANABE,Y.TANAKA,A.SUENAGA,M.KURODA,M.YAO,N.WATANABE, REMARK 1 AUTH 2 F.ARISAKA,T.OHTA,I.TANAKA,K.TSUMOTO REMARK 1 TITL STRUCTURAL BASIS FOR MULTIMERIC HEME COMPLEXATION THROUGH A REMARK 1 TITL 2 SPECIFIC PROTEIN-HEME INTERACTION: THE CASE OF THE THIRD REMARK 1 TITL 3 NEAT DOMAIN OF ISDH FROM STAPHYLOCOCCUS AUREUS. REMARK 1 REF J.BIOL.CHEM. V. 283 28649 2008 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 18667422 REMARK 1 DOI 10.1074/JBC.M803383200 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 6917 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 328 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 422 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.4940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1835 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.86000 REMARK 3 B22 (A**2) : 5.96000 REMARK 3 B33 (A**2) : -4.10000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.454 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.403 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.159 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1985 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2720 ; 1.777 ; 2.080 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 224 ; 7.338 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;38.201 ;25.319 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 324 ;19.853 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;23.801 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 288 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1512 ; 0.006 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3VTM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000095484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6932 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 51.822 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14600 REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 REMARK 200 R SYM FOR SHELL (I) : 0.41600 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: 3QUG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG-MME 3500, SODIUM IODIDE 0.2M, REMARK 280 POTASSIUM IODIDE 0.2M, PH 7.3, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.90000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.50500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.90000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASP A 546 60.64 65.31 REMARK 500 GLU A 558 -69.42 -103.97 REMARK 500 ASN A 560 49.11 -72.82 REMARK 500 GLU A 600 58.48 31.48 REMARK 500 ASP A 625 -12.15 73.81 REMARK 500 GLU B 558 -69.24 -109.44 REMARK 500 GLU B 600 19.37 44.19 REMARK 500 ASP B 610 87.57 -155.41 REMARK 500 ASP B 625 -2.03 63.79 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 3ZZ A 701 IN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 642 OH REMARK 620 2 3ZZ A 701 NB 86.0 REMARK 620 3 3ZZ A 701 NA 93.7 90.9 REMARK 620 4 3ZZ A 701 ND 96.9 175.9 91.8 REMARK 620 5 3ZZ A 701 NC 89.8 89.5 176.6 87.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 3ZZ B 701 IN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR B 642 OH REMARK 620 2 3ZZ B 701 NB 92.0 REMARK 620 3 3ZZ B 701 NA 93.5 95.1 REMARK 620 4 3ZZ B 701 ND 91.0 177.1 84.8 REMARK 620 5 3ZZ B 701 NC 88.8 85.6 177.5 94.4 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 3ZZ A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3ZZ B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QUG RELATED DB: PDB REMARK 900 STRUCTURE OF HEME TRANSPORT PROTEIN ISDH-NEAT3 FROM S. AUREUS IN REMARK 900 COMPLEX WITH GALLIUM-PORPHYRIN REMARK 900 RELATED ID: 3QUH RELATED DB: PDB REMARK 900 STRUCTURE OF HEME TRANSPORT PROTEIN ISDH-NEAT3 FROM S. AUREUS IN REMARK 900 COMPLEX WITH MANGANESE(III)-PORPHYRIN REMARK 900 RELATED ID: 2E7D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A NEAT DOMAIN FROM STAPHYLOCOCCUS AUREUS REMARK 900 RELATED ID: 2Z6F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NEAT DOMAIN FROM STAPHYLOCOCCUS AUREUS IN REMARK 900 COMPLEX WITH HEME DBREF 3VTM A 543 655 UNP Q931P4 ISDH_STAAM 543 655 DBREF 3VTM B 543 655 UNP Q931P4 ISDH_STAAM 543 655 SEQRES 1 A 113 GLN LEU THR ASP LEU GLN GLU ALA HIS PHE VAL VAL PHE SEQRES 2 A 113 GLU SER GLU GLU ASN SER GLU SER VAL MET ASP GLY PHE SEQRES 3 A 113 VAL GLU HIS PRO PHE TYR THR ALA THR LEU ASN GLY GLN SEQRES 4 A 113 LYS TYR VAL VAL MET LYS THR LYS ASP ASP SER TYR TRP SEQRES 5 A 113 LYS ASP LEU ILE VAL GLU GLY LYS ARG VAL THR THR VAL SEQRES 6 A 113 SER LYS ASP PRO LYS ASN ASN SER ARG THR LEU ILE PHE SEQRES 7 A 113 PRO TYR ILE PRO ASP LYS ALA VAL TYR ASN ALA ILE VAL SEQRES 8 A 113 LYS VAL VAL VAL ALA ASN ILE GLY TYR GLU GLY GLN TYR SEQRES 9 A 113 HIS VAL ARG ILE ILE ASN GLN ASP ILE SEQRES 1 B 113 GLN LEU THR ASP LEU GLN GLU ALA HIS PHE VAL VAL PHE SEQRES 2 B 113 GLU SER GLU GLU ASN SER GLU SER VAL MET ASP GLY PHE SEQRES 3 B 113 VAL GLU HIS PRO PHE TYR THR ALA THR LEU ASN GLY GLN SEQRES 4 B 113 LYS TYR VAL VAL MET LYS THR LYS ASP ASP SER TYR TRP SEQRES 5 B 113 LYS ASP LEU ILE VAL GLU GLY LYS ARG VAL THR THR VAL SEQRES 6 B 113 SER LYS ASP PRO LYS ASN ASN SER ARG THR LEU ILE PHE SEQRES 7 B 113 PRO TYR ILE PRO ASP LYS ALA VAL TYR ASN ALA ILE VAL SEQRES 8 B 113 LYS VAL VAL VAL ALA ASN ILE GLY TYR GLU GLY GLN TYR SEQRES 9 B 113 HIS VAL ARG ILE ILE ASN GLN ASP ILE HET 3ZZ A 701 43 HET GOL A 702 6 HET 3ZZ B 701 43 HET GOL B 702 6 HETNAM 3ZZ PROTOPORPHYRIN IX CONTAINING INDIUM HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 3ZZ 2(C34 H32 IN N4 O4) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *18(H2 O) HELIX 1 1 VAL A 564 VAL A 569 5 6 HELIX 2 2 ASP A 590 SER A 592 5 3 HELIX 3 3 PRO A 611 ASN A 614 5 4 HELIX 4 4 ALA A 638 GLY A 641 5 4 HELIX 5 5 SER B 563 VAL B 569 5 7 HELIX 6 6 ALA B 638 GLY B 641 5 4 SHEET 1 A 5 THR A 545 ALA A 550 0 SHEET 2 A 5 PHE A 573 LEU A 578 -1 O THR A 577 N THR A 545 SHEET 3 A 5 GLN A 581 LYS A 587 -1 O VAL A 585 N TYR A 574 SHEET 4 A 5 SER A 615 PRO A 621 -1 O LEU A 618 N MET A 586 SHEET 5 A 5 THR A 605 ASP A 610 -1 N VAL A 607 O THR A 617 SHEET 1 B 5 PHE A 552 GLU A 556 0 SHEET 2 B 5 TYR A 642 ASN A 652 -1 O ARG A 649 N PHE A 555 SHEET 3 B 5 VAL A 628 VAL A 637 -1 N TYR A 629 O ILE A 650 SHEET 4 B 5 TRP A 594 VAL A 599 -1 N LYS A 595 O LYS A 634 SHEET 5 B 5 LYS A 602 ARG A 603 -1 O LYS A 602 N VAL A 599 SHEET 1 C 5 THR B 545 ALA B 550 0 SHEET 2 C 5 PHE B 573 LEU B 578 -1 O THR B 577 N THR B 545 SHEET 3 C 5 GLN B 581 LYS B 587 -1 O VAL B 585 N TYR B 574 SHEET 4 C 5 SER B 615 PRO B 621 -1 O PHE B 620 N VAL B 584 SHEET 5 C 5 THR B 605 ASP B 610 -1 N SER B 608 O THR B 617 SHEET 1 D 5 PHE B 552 PHE B 555 0 SHEET 2 D 5 TYR B 642 ASN B 652 -1 O ARG B 649 N PHE B 555 SHEET 3 D 5 VAL B 628 VAL B 637 -1 N TYR B 629 O ILE B 650 SHEET 4 D 5 TRP B 594 VAL B 599 -1 N LYS B 595 O LYS B 634 SHEET 5 D 5 LYS B 602 ARG B 603 -1 O LYS B 602 N VAL B 599 LINK OH TYR A 642 IN 3ZZ A 701 1555 1555 2.06 LINK OH TYR B 642 IN 3ZZ B 701 1555 1555 2.08 CISPEP 1 HIS A 571 PRO A 572 0 2.22 CISPEP 2 HIS B 571 PRO B 572 0 0.55 SITE 1 AC1 11 GLU A 556 SER A 563 VAL A 564 PHE A 568 SITE 2 AC1 11 TRP A 594 VAL A 635 TYR A 642 TYR A 646 SITE 3 AC1 11 VAL A 648 VAL B 564 3ZZ B 701 SITE 1 AC2 6 TRP A 594 ASP A 596 LEU A 597 THR A 606 SITE 2 AC2 6 ARG A 616 HOH A 805 SITE 1 AC3 12 VAL A 564 3ZZ A 701 SER B 563 VAL B 564 SITE 2 AC3 12 PHE B 568 TYR B 593 TRP B 594 VAL B 635 SITE 3 AC3 12 ILE B 640 TYR B 642 TYR B 646 VAL B 648 SITE 1 AC4 7 ASP B 591 TRP B 594 LYS B 595 ASP B 596 SITE 2 AC4 7 LEU B 597 ARG B 616 LEU B 618 CRYST1 49.460 71.010 75.800 90.00 90.00 90.00 P 2 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 0.020218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013193 0.00000