HEADER BIOSYNTHETIC PROTEIN 15-AUG-15 5D84 TITLE STAPHYLOFERRIN B PRECURSOR BIOSYNTHETIC ENZYME SBNA BOUND TO PLP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE SIDEROPHORE BIOSYNTHESIS PROTEIN SBNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 426430; SOURCE 4 STRAIN: NEWMAN; SOURCE 5 GENE: SBNA, NWMN_0060; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS SIDEROPHORE, IRON, PLP, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.C.GRIGG,M.J.KOBYLARZ,Y.LIU,M.S.F.LEE,D.E.HEINRICHS,M.E.P.MURPHY REVDAT 3 08-JAN-20 5D84 1 JRNL REMARK REVDAT 2 24-FEB-16 5D84 1 JRNL REVDAT 1 03-FEB-16 5D84 0 JRNL AUTH M.J.KOBYLARZ,J.C.GRIGG,Y.LIU,M.S.LEE,D.E.HEINRICHS, JRNL AUTH 2 M.E.MURPHY JRNL TITL DECIPHERING THE SUBSTRATE SPECIFICITY OF SBNA, THE ENZYME JRNL TITL 2 CATALYZING THE FIRST STEP IN STAPHYLOFERRIN B BIOSYNTHESIS. JRNL REF BIOCHEMISTRY V. 55 927 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 26794841 JRNL DOI 10.1021/ACS.BIOCHEM.5B01045 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 48724 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) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2598 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3421 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 192 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2456 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : -0.35000 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): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.585 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2714 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3705 ; 1.515 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 358 ; 5.436 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;36.923 ;25.089 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 492 ;12.462 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.178 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2061 ; 0.009 ; 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): 1375 ; 2.627 ; 1.485 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1752 ; 3.327 ; 2.245 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1339 ; 3.354 ; 1.782 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): 2714 ; 3.049 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 89 ;42.449 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2922 ;16.278 ; 5.000 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5D84 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97952 REMARK 200 MONOCHROMATOR : ACCEL/BRUKER DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR (DCM), FEATURING REMARK 200 INDIRECTLY CRYO-COOLED FIRST REMARK 200 CRYSTAL AND SAGITTALLY FOCUSING REMARK 200 SECOND CRYSTAL REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR: ULTRA REMARK 200 -LOW EXPANSION (ULE) TITANIUM REMARK 200 SILIICATE FLAT MIRROR WITH PT, REMARK 200 UNCOATED, AND PD STRIPS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51631 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 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: PHENIX 2.2.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.5, 0.2 M MGCL2, 20 REMARK 280 -25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z 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 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 28.04000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.91400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.04000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.91400 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: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 56.08000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1236 LIES ON A SPECIAL POSITION. 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 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 SER A 5 REMARK 465 GLN A 6 REMARK 465 SER A 325 REMARK 465 GLU A 326 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 OD2 ASP A 263 O HOH A 1101 2.16 REMARK 500 NH2 ARG A 303 O HOH A 1102 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 276 CG1 - CB - CG2 ANGL. DEV. = -13.3 DEGREES 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 ASN A 41 151.22 -49.35 REMARK 500 ALA A 124 -34.12 -23.59 REMARK 500 ASP A 145 73.10 59.81 REMARK 500 SER A 185 -68.56 -138.07 REMARK 500 LEU A 307 -113.39 -115.35 REMARK 500 GLN A 321 28.42 -55.45 REMARK 500 GLN A 321 15.69 -49.08 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 A1462 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A1463 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A1464 DISTANCE = 7.10 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 MG A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1427 O REMARK 620 2 HOH A1460 O 87.2 REMARK 620 3 HOH A1137 O 86.9 95.7 REMARK 620 4 HOH A1179 O 90.5 174.4 89.2 REMARK 620 5 HOH A1400 O 172.6 95.3 86.0 87.7 REMARK 620 6 HOH A1461 O 91.9 86.2 177.7 88.8 95.1 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 PLP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D85 RELATED DB: PDB REMARK 900 RELATED ID: 5D86 RELATED DB: PDB REMARK 900 RELATED ID: 5D87 RELATED DB: PDB DBREF 5D84 A 1 326 UNP A6QDA0 SBNA_STAAE 1 326 SEQRES 1 A 326 MET ILE GLU LYS SER GLN ALA CYS HIS ASP SER LEU LEU SEQRES 2 A 326 ASP SER VAL GLY GLN THR PRO MET VAL GLN LEU HIS GLN SEQRES 3 A 326 LEU PHE PRO LYS HIS GLU VAL PHE ALA LYS LEU GLU TYR SEQRES 4 A 326 MET ASN PRO GLY GLY SER MET LYS ASP ARG PRO ALA LYS SEQRES 5 A 326 TYR ILE ILE GLU HIS GLY ILE LYS HIS GLY LEU ILE THR SEQRES 6 A 326 GLU ASN THR HIS LEU ILE GLU SER THR SER GLY ASN LEU SEQRES 7 A 326 GLY ILE ALA LEU ALA MET ILE ALA LYS ILE LYS GLY LEU SEQRES 8 A 326 LYS LEU THR CYS VAL VAL ASP PRO LYS ILE SER PRO THR SEQRES 9 A 326 ASN LEU LYS ILE ILE LYS SER TYR GLY ALA ASN VAL GLU SEQRES 10 A 326 MET VAL GLU GLU PRO ASP ALA HIS GLY GLY TYR LEU MET SEQRES 11 A 326 THR ARG ILE ALA LYS VAL GLN GLU LEU LEU ALA THR ILE SEQRES 12 A 326 ASP ASP ALA TYR TRP ILE ASN GLN TYR ALA ASN GLU LEU SEQRES 13 A 326 ASN TRP GLN SER HIS TYR HIS GLY ALA GLY THR GLU ILE SEQRES 14 A 326 VAL GLU THR ILE LYS GLN PRO ILE ASP TYR PHE VAL ALA SEQRES 15 A 326 PRO VAL SER THR THR GLY SER ILE MET GLY MET SER ARG SEQRES 16 A 326 LYS ILE LYS GLU VAL HIS PRO ASN ALA GLN ILE VAL ALA SEQRES 17 A 326 VAL ASP ALA LYS GLY SER VAL ILE PHE GLY ASP LYS PRO SEQRES 18 A 326 ILE ASN ARG GLU LEU PRO GLY ILE GLY ALA SER ARG VAL SEQRES 19 A 326 PRO GLU ILE LEU ASN ARG SER GLU ILE ASN GLN VAL ILE SEQRES 20 A 326 HIS VAL ASP ASP TYR GLN SER ALA LEU GLY CYS ARG LYS SEQRES 21 A 326 LEU ILE ASP TYR GLU GLY ILE PHE ALA GLY GLY SER THR SEQRES 22 A 326 GLY SER ILE ILE ALA ALA ILE GLU GLN LEU ILE THR SER SEQRES 23 A 326 ILE GLU GLU GLY ALA THR ILE VAL THR ILE LEU PRO ASP SEQRES 24 A 326 ARG GLY ASP ARG TYR LEU ASP LEU VAL TYR SER ASP THR SEQRES 25 A 326 TRP LEU GLU LYS MET LYS SER ARG GLN GLY VAL LYS SER SEQRES 26 A 326 GLU HET PLP A1001 15 HET MG A1002 1 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MG MAGNESIUM ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 MG MG 2+ FORMUL 4 HOH *364(H2 O) HELIX 1 AA1 SER A 11 VAL A 16 5 6 HELIX 2 AA2 GLU A 38 ASN A 41 5 4 HELIX 3 AA3 LYS A 47 HIS A 61 1 15 HELIX 4 AA4 GLY A 76 GLY A 90 1 15 HELIX 5 AA5 SER A 102 TYR A 112 1 11 HELIX 6 AA6 TYR A 128 ILE A 143 1 16 HELIX 7 AA7 ASN A 154 GLY A 164 1 11 HELIX 8 AA8 GLY A 164 ILE A 173 1 10 HELIX 9 AA9 THR A 187 HIS A 201 1 15 HELIX 10 AB1 ASN A 239 ILE A 243 5 5 HELIX 11 AB2 ASP A 250 GLY A 266 1 17 HELIX 12 AB3 GLY A 270 THR A 285 1 16 HELIX 13 AB4 ARG A 300 LEU A 305 5 6 HELIX 14 AB5 SER A 310 GLN A 321 1 12 SHEET 1 AA1 6 MET A 21 GLN A 23 0 SHEET 2 AA1 6 GLU A 32 LYS A 36 -1 O ALA A 35 N VAL A 22 SHEET 3 AA1 6 THR A 292 ILE A 296 1 O ILE A 293 N PHE A 34 SHEET 4 AA1 6 TYR A 179 PRO A 183 1 N VAL A 181 O VAL A 294 SHEET 5 AA1 6 GLN A 205 ALA A 211 1 O VAL A 207 N PHE A 180 SHEET 6 AA1 6 GLN A 245 VAL A 249 1 O ILE A 247 N ALA A 208 SHEET 1 AA2 4 ASN A 115 MET A 118 0 SHEET 2 AA2 4 LEU A 93 VAL A 97 1 N LEU A 93 O ASN A 115 SHEET 3 AA2 4 HIS A 69 SER A 73 1 N GLU A 72 O VAL A 96 SHEET 4 AA2 4 ALA A 146 TRP A 148 1 O TYR A 147 N ILE A 71 LINK NZ LYS A 47 C4A PLP A1001 1555 1555 1.26 LINK MG MG A1002 O HOH A1427 1555 1555 2.10 LINK MG MG A1002 O HOH A1460 1555 1555 2.13 LINK MG MG A1002 O HOH A1137 1555 1555 2.08 LINK MG MG A1002 O HOH A1179 1555 1555 2.12 LINK MG MG A1002 O HOH A1400 1555 1555 2.15 LINK MG MG A1002 O HOH A1461 1555 1555 2.05 SITE 1 AC1 15 LYS A 47 ASN A 77 VAL A 184 SER A 185 SITE 2 AC1 15 THR A 186 THR A 187 GLY A 188 SER A 189 SITE 3 AC1 15 GLY A 228 SER A 272 PRO A 298 ASP A 299 SITE 4 AC1 15 HOH A1138 HOH A1190 HOH A1238 SITE 1 AC2 6 HOH A1137 HOH A1179 HOH A1400 HOH A1427 SITE 2 AC2 6 HOH A1460 HOH A1461 CRYST1 56.080 115.828 45.138 90.00 90.00 90.00 P 21 21 2 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 0.017832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022154 0.00000