HEADER METAL BINDING PROTEIN 27-SEP-17 5YH8 TITLE THE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS CNTA IN COMPLEX WITH TITLE 2 STAPHYLOPINE AND NICKEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICKEL ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 26-532; COMPND 5 SYNONYM: NICKEL ABC TRANSPORTER,PERIPLASMIC NICKEL-BINDING PROTEIN, COMPND 6 OLIGOPEPTIDE TRANSPORTER PUTATIVE SUBSTRATE BINDING DOMAIN PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: OPP-1A, AYM28_13740, AYM37_13740, ERS072738_00487, SOURCE 5 ERS074020_00717, HMPREF3211_02361; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, RECEPTOR, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.JI,L.SONG REVDAT 4 27-MAR-24 5YH8 1 REMARK REVDAT 3 25-APR-18 5YH8 1 JRNL REVDAT 2 11-APR-18 5YH8 1 JRNL REVDAT 1 28-MAR-18 5YH8 0 JRNL AUTH L.SONG,Y.ZHANG,W.CHEN,T.GU,S.Y.ZHANG,Q.JI JRNL TITL MECHANISTIC INSIGHTS INTO STAPHYLOPINE-MEDIATED METAL JRNL TITL 2 ACQUISITION JRNL REF PROC. NATL. ACAD. SCI. V. 115 3942 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29581261 JRNL DOI 10.1073/PNAS.1718382115 REMARK 2 REMARK 2 RESOLUTION. 2.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28663 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1588 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) : 2.12 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2055 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4064 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.03000 REMARK 3 B22 (A**2) : -2.13000 REMARK 3 B33 (A**2) : 0.10000 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): 0.218 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.733 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 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): 4224 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4061 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5643 ; 1.822 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9437 ; 1.104 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 7.135 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;40.892 ;26.071 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 809 ;15.946 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ; 6.844 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4672 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 885 ; 0.002 ; 0.020 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): 2042 ; 2.588 ; 3.164 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2042 ; 2.588 ; 3.164 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2549 ; 3.730 ; 4.737 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2550 ; 3.730 ; 4.737 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2182 ; 3.696 ; 3.678 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2182 ; 3.696 ; 3.678 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3095 ; 5.792 ; 5.280 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4953 ; 7.485 ;25.779 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4953 ; 7.484 ;25.780 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 : 1.20 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 5YH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30251 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.120 REMARK 200 RESOLUTION RANGE LOW (A) : 70.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 3.5, 14% (W/V) REMARK 280 POLYETHYLENE GLYCOL 1000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 42.73700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.15750 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.73700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.15750 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 LEU A 52 -108.62 -140.16 REMARK 500 TYR A 129 95.06 -160.82 REMARK 500 TYR A 142 53.33 -92.57 REMARK 500 PHE A 162 61.76 -119.41 REMARK 500 GLU A 177 -55.31 -131.24 REMARK 500 ALA A 204 -159.98 -77.16 REMARK 500 ASP A 319 92.44 -168.57 REMARK 500 ASN A 434 32.41 -88.94 REMARK 500 ILE A 474 -58.13 -123.24 REMARK 500 TYR A 506 -3.40 106.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1024 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A1025 DISTANCE = 7.35 ANGSTROMS 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 NI A 601 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 8UX A 602 OAC REMARK 620 2 8UX A 602 OXT 91.4 REMARK 620 3 8UX A 602 N 81.7 81.1 REMARK 620 4 8UX A 602 NAN 95.3 172.5 96.5 REMARK 620 5 8UX A 602 OAG 173.9 90.8 93.0 82.2 REMARK 620 6 8UX A 602 NAP 94.3 94.0 173.5 88.9 91.3 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 NI A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8UX A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 613 DBREF1 5YH8 A 1 507 UNP A0A068A9N4_STAAU DBREF2 5YH8 A A0A068A9N4 26 532 SEQADV 5YH8 PRO A -2 UNP A0A068A9N EXPRESSION TAG SEQADV 5YH8 HIS A -1 UNP A0A068A9N EXPRESSION TAG SEQADV 5YH8 MET A 0 UNP A0A068A9N EXPRESSION TAG SEQRES 1 A 510 PRO HIS MET GLY LEU GLU GLU LYS LYS GLU ASN LYS GLN SEQRES 2 A 510 LEU THR TYR THR THR VAL LYS ASP ILE GLY ASP MET ASN SEQRES 3 A 510 PRO HIS VAL TYR GLY GLY SER MET SER ALA GLU SER MET SEQRES 4 A 510 ILE TYR GLU PRO LEU VAL ARG ASN THR LYS ASP GLY ILE SEQRES 5 A 510 LYS PRO LEU LEU ALA LYS LYS TRP ASP VAL SER GLU ASP SEQRES 6 A 510 GLY LYS THR TYR THR PHE HIS LEU ARG ASP ASP VAL LYS SEQRES 7 A 510 PHE HIS ASP GLY THR PRO PHE ASP ALA ASP ALA VAL LYS SEQRES 8 A 510 LYS ASN ILE ASP ALA VAL GLN GLU ASN LYS LYS LEU HIS SEQRES 9 A 510 SER TRP LEU LYS ILE SER THR LEU ILE ASP ASN VAL LYS SEQRES 10 A 510 VAL LYS ASP LYS TYR THR VAL GLU LEU ASN LEU LYS GLU SEQRES 11 A 510 ALA TYR GLN PRO ALA LEU ALA GLU LEU ALA MET PRO ARG SEQRES 12 A 510 PRO TYR VAL PHE VAL SER PRO LYS ASP PHE LYS ASN GLY SEQRES 13 A 510 THR THR LYS ASP GLY VAL LYS LYS PHE ASP GLY THR GLY SEQRES 14 A 510 PRO PHE LYS LEU GLY GLU HIS LYS LYS ASP GLU SER ALA SEQRES 15 A 510 ASP PHE ASN LYS ASN ASP GLN TYR TRP GLY GLU LYS SER SEQRES 16 A 510 LYS LEU ASN LYS VAL GLN ALA LYS VAL MET PRO ALA GLY SEQRES 17 A 510 GLU THR ALA PHE LEU SER MET LYS LYS GLY GLU THR ASN SEQRES 18 A 510 PHE ALA PHE THR ASP ASP ARG GLY THR ASP SER LEU ASP SEQRES 19 A 510 LYS ASP SER LEU LYS GLN LEU LYS ASP THR GLY ASP TYR SEQRES 20 A 510 GLN VAL LYS ARG SER GLN PRO MET ASN THR LYS MET LEU SEQRES 21 A 510 VAL VAL ASN SER GLY LYS LYS ASP ASN ALA VAL SER ASP SEQRES 22 A 510 LYS THR VAL ARG GLN ALA ILE GLY HIS MET VAL ASN ARG SEQRES 23 A 510 ASP LYS ILE ALA LYS GLU ILE LEU ASP GLY GLN GLU LYS SEQRES 24 A 510 PRO ALA THR GLN LEU PHE ALA LYS ASN VAL THR ASP ILE SEQRES 25 A 510 ASN PHE ASP MET PRO THR ARG LYS TYR ASP LEU LYS LYS SEQRES 26 A 510 ALA GLU SER LEU LEU ASP GLU ALA GLY TRP LYS LYS GLY SEQRES 27 A 510 LYS ASP SER ASP VAL ARG GLN LYS ASP GLY LYS ASN LEU SEQRES 28 A 510 GLU MET ALA MET TYR TYR ASP LYS GLY SER SER SER GLN SEQRES 29 A 510 LYS GLU GLN ALA GLU TYR LEU GLN ALA GLU PHE LYS LYS SEQRES 30 A 510 MET GLY ILE LYS LEU ASN ILE ASN GLY GLU THR SER ASP SEQRES 31 A 510 LYS ILE ALA GLU ARG ARG THR SER GLY ASP TYR ASP LEU SEQRES 32 A 510 MET PHE ASN GLN THR TRP GLY LEU LEU TYR ASP PRO GLN SEQRES 33 A 510 SER THR ILE ALA ALA PHE LYS ALA LYS ASN GLY TYR GLU SEQRES 34 A 510 SER ALA THR SER GLY ILE GLU ASN LYS ASP LYS ILE TYR SEQRES 35 A 510 ASN SER ILE ASP ASP ALA PHE LYS ILE GLN ASN GLY LYS SEQRES 36 A 510 GLU ARG SER ASP ALA TYR LYS ASN ILE LEU LYS GLN ILE SEQRES 37 A 510 ASP ASP GLU GLY ILE PHE ILE PRO ILE SER HIS GLY SER SEQRES 38 A 510 MET THR VAL VAL ALA PRO LYS ASP LEU GLU LYS VAL SER SEQRES 39 A 510 PHE THR GLN SER GLN TYR GLU LEU PRO PHE ASN GLU MET SEQRES 40 A 510 GLN TYR LYS HET NI A 601 1 HET 8UX A 602 23 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET GOL A 608 6 HET GOL A 609 6 HET GOL A 610 6 HET GOL A 611 6 HET PEG A 612 7 HET PEG A 613 7 HETNAM NI NICKEL (II) ION HETNAM 8UX (2~{S})-4-[[(2~{R})-3-(1~{H}-IMIDAZOL-4-YL)-1-OXIDANYL- HETNAM 2 8UX 1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]-2-[[(2~{S})-1- HETNAM 3 8UX OXIDANYL-1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]BUTANOIC HETNAM 4 8UX ACID HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN 8UX STAPHYLOPINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NI NI 2+ FORMUL 3 8UX C13 H20 N4 O6 FORMUL 4 GOL 9(C3 H8 O3) FORMUL 13 PEG 2(C4 H10 O3) FORMUL 15 HOH *325(H2 O) HELIX 1 AA1 PRO A -2 ASN A 8 1 11 HELIX 2 AA2 SER A 30 TYR A 38 1 9 HELIX 3 AA3 ASP A 83 GLN A 95 1 13 HELIX 4 AA4 GLU A 96 SER A 102 5 7 HELIX 5 AA5 LEU A 104 THR A 108 5 5 HELIX 6 AA6 PRO A 131 ALA A 137 1 7 HELIX 7 AA7 SER A 146 PHE A 150 5 5 HELIX 8 AA8 GLY A 205 LYS A 214 1 10 HELIX 9 AA9 ASP A 231 THR A 241 1 11 HELIX 10 AB1 ASN A 266 SER A 269 5 4 HELIX 11 AB2 ASP A 270 HIS A 279 1 10 HELIX 12 AB3 ASN A 282 ILE A 290 1 9 HELIX 13 AB4 ASP A 319 ALA A 330 1 12 HELIX 14 AB5 SER A 358 MET A 375 1 18 HELIX 15 AB6 THR A 385 GLY A 396 1 12 HELIX 16 AB7 PRO A 412 ALA A 418 1 7 HELIX 17 AB8 PHE A 419 ALA A 421 5 3 HELIX 18 AB9 TYR A 425 SER A 430 1 6 HELIX 19 AC1 ASN A 434 PHE A 446 1 13 HELIX 20 AC2 ASN A 450 GLY A 469 1 20 SHEET 1 AA1 4 GLN A 10 THR A 15 0 SHEET 2 AA1 4 LYS A 196 VAL A 201 1 O LYS A 200 N TYR A 13 SHEET 3 AA1 4 SER A 178 LYS A 183 -1 N ALA A 179 O ALA A 199 SHEET 4 AA1 4 PHE A 168 LYS A 174 -1 N GLY A 171 O ASP A 180 SHEET 1 AA2 2 VAL A 42 THR A 45 0 SHEET 2 AA2 2 GLY A 48 PRO A 51 -1 O LYS A 50 N ARG A 43 SHEET 1 AA3 4 ALA A 54 VAL A 59 0 SHEET 2 AA3 4 THR A 65 LEU A 70 -1 O THR A 67 N ASP A 58 SHEET 3 AA3 4 THR A 120 LEU A 125 -1 O VAL A 121 N PHE A 68 SHEET 4 AA3 4 ILE A 110 ASP A 117 -1 N ASP A 111 O ASN A 124 SHEET 1 AA4 3 ALA A 220 PHE A 221 0 SHEET 2 AA4 3 SER A 478 PRO A 484 -1 O VAL A 482 N ALA A 220 SHEET 3 AA4 3 TYR A 244 PRO A 251 -1 N LYS A 247 O VAL A 481 SHEET 1 AA5 5 LYS A 378 GLU A 384 0 SHEET 2 AA5 5 GLU A 349 ASP A 355 1 N TYR A 354 O GLU A 384 SHEET 3 AA5 5 LEU A 400 GLN A 404 1 O PHE A 402 N TYR A 353 SHEET 4 AA5 5 LYS A 255 VAL A 259 -1 N VAL A 258 O MET A 401 SHEET 5 AA5 5 PHE A 471 SER A 475 -1 O SER A 475 N LYS A 255 SHEET 1 AA6 2 GLN A 342 LYS A 343 0 SHEET 2 AA6 2 LYS A 346 ASN A 347 -1 O LYS A 346 N LYS A 343 LINK NI NI A 601 OAC 8UX A 602 1555 1555 2.02 LINK NI NI A 601 OXT 8UX A 602 1555 1555 1.97 LINK NI NI A 601 N 8UX A 602 1555 1555 2.11 LINK NI NI A 601 NAN 8UX A 602 1555 1555 2.27 LINK NI NI A 601 OAG 8UX A 602 1555 1555 2.04 LINK NI NI A 601 NAP 8UX A 602 1555 1555 2.09 CISPEP 1 ARG A 140 PRO A 141 0 7.07 CISPEP 2 ASP A 411 PRO A 412 0 -2.64 SITE 1 AC1 1 8UX A 602 SITE 1 AC2 15 TYR A 27 TRP A 103 ARG A 140 ASP A 224 SITE 2 AC2 15 ARG A 225 ARG A 393 TRP A 406 ASN A 423 SITE 3 AC2 15 TYR A 497 NI A 601 GOL A 611 HOH A 749 SITE 4 AC2 15 HOH A 752 HOH A 803 HOH A 881 SITE 1 AC3 8 TRP A 103 LYS A 105 TYR A 129 GLU A 135 SITE 2 AC3 8 GLN A 413 SER A 414 ALA A 417 PHE A 446 SITE 1 AC4 4 GLN A 275 HIS A 279 ARG A 316 HOH A 714 SITE 1 AC5 4 LYS A 89 PRO A 147 HOH A 744 HOH A 966 SITE 1 AC6 7 THR A 299 GLN A 300 LYS A 304 ASP A 312 SITE 2 AC6 7 HIS A 476 HOH A 701 HOH A 729 SITE 1 AC7 5 LYS A 239 ALA A 370 GLU A 371 LYS A 374 SITE 2 AC7 5 LYS A 485 SITE 1 AC8 6 LYS A 151 ASN A 152 LYS A 160 GLU A 366 SITE 2 AC8 6 ILE A 381 HOH A 808 SITE 1 AC9 5 HIS A -1 PRO A -2 LYS A 151 ASP A 243 SITE 2 AC9 5 LYS A 373 SITE 1 AD1 5 LYS A 263 ASP A 265 ASP A 399 HOH A 805 SITE 2 AD1 5 HOH A 878 SITE 1 AD2 6 TYR A 27 ARG A 225 ARG A 393 THR A 394 SITE 2 AD2 6 ASN A 423 8UX A 602 SITE 1 AD3 8 ARG A 43 ASN A 44 ALA A 137 PRO A 139 SITE 2 AD3 8 LEU A 409 GLU A 498 HOH A 780 HOH A 948 SITE 1 AD4 8 ASP A 228 LEU A 230 LEU A 235 ARG A 248 SITE 2 AD4 8 GLN A 294 GLU A 295 SER A 360 THR A 480 CRYST1 70.782 85.474 86.315 90.00 90.00 90.00 P 2 21 21 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 0.014128 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011585 0.00000