10 20 30 40 50 60 70 80 3VFL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 10-JAN-12 3VFL
TITLE STRUCTURE, FUNCTION, STABILITY AND KNOCKOUT PHENOTYPE OF TITLE 2 DIHYDRODIPICOLINATE SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.2.1.52; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 406556; SOURCE 4 STRAIN: A5LD17; SOURCE 5 GENE: CGSSP3BS71_00085, DAPA; 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: PET101/D-TOPO
KEYWDS LYASE, DIHYDRODIPICOLINATE SYNTHASE, LYSINE BIOSYNTHESIS
EXPDTA X-RAY DIFFRACTION
AUTHOR M.A.GORMAN
REVDAT 1 12-JUN-13 3VFL 0
SPRSDE 12-JUN-13 3VFL 3H5D
JRNL AUTH C.DOGOVSKI,M.A.GORMAN,N.E.KETAREN,J.PRASZKIER,G.BRYANT, JRNL AUTH 2 J.YANG,M.D.W.GRIFFIN,F.G.PEARCE,S.K.BHARGAVA,R.C.J.DOBSON, JRNL AUTH 3 C.A.HUTTON,J.A.GERRARD,R.M.ROBINS-BROWNE,G.B.JAMESON, JRNL AUTH 4 M.W.PARKER,M.A.PERUGINI JRNL TITL STRUCTURE, FUNCTION, STABILITY AND KNOCKOUT PHENOTYPE OF JRNL TITL 2 DIHYDRODIPICOLINATE SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.E.SIBARANI,M.A.GORMAN,C.DOGOVSKI,M.W.PARKER,M.A.PERUGINI REMARK 1 TITL CRYSTALLIZATION OF DIHYDRODIPICOLINATE SYNTHASE FROM A REMARK 1 TITL 2 CLINICAL ISOLATE OF STREPTOCOCCUS PNEUMONIAE. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 66 32 2010 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 20057065 REMARK 1 DOI 10.1107/S174430910904771X
REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 51243 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2792 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3410 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 189 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4720 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 26.22000 REMARK 3 B22 (A**2) : -14.27000 REMARK 3 B33 (A**2) : -11.95000 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): 0.027 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.694 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4878 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6635 ; 2.417 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 612 ; 7.621 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;38.198 ;25.024 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 780 ;15.876 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;20.502 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 764 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3680 ; 0.013 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 0 A 2 A 296 0 REMARK 3 0 B 2 B 296 0 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.541 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H, L, K REMARK 3 TWIN FRACTION : 0.459 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 3VFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-12. REMARK 100 THE RCSB ID CODE IS RCSB069983.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.954 REMARK 200 MONOCHROMATOR : SILICON 1 1 1 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54089 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 74.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.670 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: PDB ENTRY 3HIJ REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM CHLORIDE, 20% (W/V) PEG REMARK 280 6000, 0.1M MES PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 52.66600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.75500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.66600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.75500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 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 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 LYS A 300 REMARK 465 ALA A 301 REMARK 465 MET B 1 REMARK 465 ALA B 298 REMARK 465 THR B 299 REMARK 465 LYS B 300 REMARK 465 ALA B 301
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 125 CG HIS A 125 CD2 0.061 REMARK 500 HIS B 59 CG HIS B 59 CD2 0.065 REMARK 500 HIS B 125 NE2 HIS B 125 CD2 -0.067 REMARK 500 HIS B 182 CG HIS B 182 CD2 0.055 REMARK 500 HIS B 199 CG HIS B 199 CD2 0.075 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 ASP A 22 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 60 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 131 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 196 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 LEU A 203 CB - CG - CD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 LEU A 274 CB - CG - CD1 ANGL. DEV. = -10.2 DEGREES REMARK 500 LEU B 33 CB - CG - CD1 ANGL. DEV. = -12.1 DEGREES REMARK 500 ASP B 160 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 LEU B 188 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ASP B 196 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP B 206 CB - CG - OD1 ANGL. DEV. = -5.4 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 ILE A 16 172.65 -59.02 REMARK 500 ASN A 74 56.35 29.94 REMARK 500 THR A 85 -167.45 -126.18 REMARK 500 ALA A 106 153.20 178.62 REMARK 500 TYR A 114 -55.46 72.40 REMARK 500 ILE A 142 73.84 -151.08 REMARK 500 VAL A 147 -66.11 66.24 REMARK 500 THR A 171 -105.82 -122.30 REMARK 500 ASP A 310 1.77 -62.57 REMARK 500 SER B 54 -39.25 -33.50 REMARK 500 TYR B 114 -57.61 74.96 REMARK 500 ILE B 142 82.90 -153.72 REMARK 500 VAL B 147 -56.52 78.74 REMARK 500 THR B 171 -87.94 -123.60 REMARK 500 ASP B 231 74.42 -112.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 SER B 54 24.5 L L OUTSIDE RANGE 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 K B 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE B 164 O REMARK 620 2 ALA B 159 O 102.8 REMARK 620 3 HIS B 161 O 88.2 88.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 62 OE2 REMARK 620 2 SER A 54 O 92.9 REMARK 620 3 LEU A 57 O 89.6 92.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 161 O REMARK 620 2 ILE A 164 O 89.5 REMARK 620 3 ALA A 159 O 89.1 100.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 57 O REMARK 620 2 HOH B 572 O 176.9 REMARK 620 3 SER B 54 O 89.0 89.8 REMARK 620 4 GLU B 62 OE2 85.0 97.8 85.5 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 K A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 404
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BI8 RELATED DB: PDB REMARK 900 STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM CLOSTRIDIUM REMARK 900 BOTULINUM REMARK 900 RELATED ID: 3DU0 RELATED DB: PDB REMARK 900 E. COLI DIHYDRODIPICOLINATE SYNTHASE WITH FIRST SUBSTRATE, REMARK 900 PYRUVATE, BOUND IN ACTIVE SITE REMARK 900 RELATED ID: 3HIJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM REMARK 900 BACILLUS ANTHRACIS IN COMPLEX WITH ITS SUBSTRATE, PYRUVATE
DBREF 3VFL A 1 311 UNP A5LD17 A5LD17_STRPN 1 311 DBREF 3VFL B 1 311 UNP A5LD17 A5LD17_STRPN 1 311
SEQRES 1 A 311 MET SER TYR GLN ASP LEU LYS GLU CYS LYS ILE ILE THR SEQRES 2 A 311 ALA PHE ILE THR PRO PHE HIS GLU ASP GLY SER ILE ASN SEQRES 3 A 311 PHE ASP ALA ILE PRO ALA LEU ILE GLU HIS LEU LEU ALA SEQRES 4 A 311 HIS HIS THR ASP GLY ILE LEU LEU ALA GLY THR THR ALA SEQRES 5 A 311 GLU SER PRO THR LEU THR HIS ASP GLU GLU LEU GLU LEU SEQRES 6 A 311 PHE ALA ALA VAL GLN LYS VAL VAL ASN GLY ARG VAL PRO SEQRES 7 A 311 LEU ILE ALA GLY VAL GLY THR ASN ASP THR ARG ASP SER SEQRES 8 A 311 ILE GLU PHE VAL LYS GLU VAL ALA GLU PHE GLY GLY PHE SEQRES 9 A 311 ALA ALA GLY LEU ALA ILE VAL PRO TYR TYR ASN LYS PRO SEQRES 10 A 311 SER GLN GLU GLY MET TYR GLN HIS PHE LYS ALA ILE ALA SEQRES 11 A 311 ASP ALA SER ASP LEU PRO ILE ILE ILE TYR ASN ILE PRO SEQRES 12 A 311 GLY ARG VAL VAL VAL GLU LEU THR PRO GLU THR MET LEU SEQRES 13 A 311 ARG LEU ALA ASP HIS PRO ASN ILE ILE GLY VAL LYS GLU SEQRES 14 A 311 CYS THR SER LEU ALA ASN MET ALA TYR LEU ILE GLU HIS SEQRES 15 A 311 LYS PRO GLU GLU PHE LEU ILE TYR THR GLY GLU ASP GLY SEQRES 16 A 311 ASP ALA PHE HIS ALA MET ASN LEU GLY ALA ASP GLY VAL SEQRES 17 A 311 ILE SER VAL ALA SER HIS THR ASN GLY ASP GLU MET HIS SEQRES 18 A 311 GLU MET PHE THR ALA ILE ALA GLU SER ASP MET LYS LYS SEQRES 19 A 311 ALA ALA ALA ILE GLN ARG LYS PHE ILE PRO LYS VAL ASN SEQRES 20 A 311 ALA LEU PHE SER TYR PRO SER PRO ALA PRO VAL LYS ALA SEQRES 21 A 311 ILE LEU ASN TYR MET GLY PHE GLU ALA GLY PRO THR ARG SEQRES 22 A 311 LEU PRO LEU VAL PRO ALA PRO GLU GLU ASP VAL LYS ARG SEQRES 23 A 311 ILE ILE LYS VAL VAL VAL ASP GLY ASP TYR GLU ALA THR SEQRES 24 A 311 LYS ALA THR VAL THR GLY VAL LEU ARG PRO ASP TYR SEQRES 1 B 311 MET SER TYR GLN ASP LEU LYS GLU CYS LYS ILE ILE THR SEQRES 2 B 311 ALA PHE ILE THR PRO PHE HIS GLU ASP GLY SER ILE ASN SEQRES 3 B 311 PHE ASP ALA ILE PRO ALA LEU ILE GLU HIS LEU LEU ALA SEQRES 4 B 311 HIS HIS THR ASP GLY ILE LEU LEU ALA GLY THR THR ALA SEQRES 5 B 311 GLU SER PRO THR LEU THR HIS ASP GLU GLU LEU GLU LEU SEQRES 6 B 311 PHE ALA ALA VAL GLN LYS VAL VAL ASN GLY ARG VAL PRO SEQRES 7 B 311 LEU ILE ALA GLY VAL GLY THR ASN ASP THR ARG ASP SER SEQRES 8 B 311 ILE GLU PHE VAL LYS GLU VAL ALA GLU PHE GLY GLY PHE SEQRES 9 B 311 ALA ALA GLY LEU ALA ILE VAL PRO TYR TYR ASN LYS PRO SEQRES 10 B 311 SER GLN GLU GLY MET TYR GLN HIS PHE LYS ALA ILE ALA SEQRES 11 B 311 ASP ALA SER ASP LEU PRO ILE ILE ILE TYR ASN ILE PRO SEQRES 12 B 311 GLY ARG VAL VAL VAL GLU LEU THR PRO GLU THR MET LEU SEQRES 13 B 311 ARG LEU ALA ASP HIS PRO ASN ILE ILE GLY VAL LYS GLU SEQRES 14 B 311 CYS THR SER LEU ALA ASN MET ALA TYR LEU ILE GLU HIS SEQRES 15 B 311 LYS PRO GLU GLU PHE LEU ILE TYR THR GLY GLU ASP GLY SEQRES 16 B 311 ASP ALA PHE HIS ALA MET ASN LEU GLY ALA ASP GLY VAL SEQRES 17 B 311 ILE SER VAL ALA SER HIS THR ASN GLY ASP GLU MET HIS SEQRES 18 B 311 GLU MET PHE THR ALA ILE ALA GLU SER ASP MET LYS LYS SEQRES 19 B 311 ALA ALA ALA ILE GLN ARG LYS PHE ILE PRO LYS VAL ASN SEQRES 20 B 311 ALA LEU PHE SER TYR PRO SER PRO ALA PRO VAL LYS ALA SEQRES 21 B 311 ILE LEU ASN TYR MET GLY PHE GLU ALA GLY PRO THR ARG SEQRES 22 B 311 LEU PRO LEU VAL PRO ALA PRO GLU GLU ASP VAL LYS ARG SEQRES 23 B 311 ILE ILE LYS VAL VAL VAL ASP GLY ASP TYR GLU ALA THR SEQRES 24 B 311 LYS ALA THR VAL THR GLY VAL LEU ARG PRO ASP TYR
HET K A 401 1 HET K A 402 1 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET MES A 406 12 HET K B 401 1 HET K B 402 1 HET GOL B 403 6 HET MES B 404 12
HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 K 4(K 1+) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 8 MES 2(C6 H13 N O4 S) FORMUL 13 HOH *237(H2 O)
HELIX 1 1 SER A 2 LYS A 7 1 6 HELIX 2 2 ALA A 29 HIS A 40 1 12 HELIX 3 3 GLY A 49 LEU A 57 5 9 HELIX 4 4 THR A 58 ASN A 74 1 17 HELIX 5 5 ASP A 87 GLY A 102 1 16 HELIX 6 6 SER A 118 ALA A 132 1 15 HELIX 7 7 ILE A 142 VAL A 147 1 6 HELIX 8 8 THR A 151 ASP A 160 1 10 HELIX 9 9 SER A 172 LYS A 183 1 12 HELIX 10 10 GLU A 193 GLY A 195 5 3 HELIX 11 11 ASP A 196 LEU A 203 1 8 HELIX 12 12 ALA A 212 GLU A 229 1 18 HELIX 13 13 ASP A 231 PHE A 250 1 20 HELIX 14 14 PRO A 255 MET A 265 1 11 HELIX 15 15 PRO A 280 ASP A 293 1 14 HELIX 16 16 TYR B 3 LYS B 7 1 5 HELIX 17 17 ASN B 26 ASP B 28 5 3 HELIX 18 18 ALA B 29 ALA B 39 1 11 HELIX 19 19 GLU B 53 LEU B 57 5 5 HELIX 20 20 THR B 58 ASN B 74 1 17 HELIX 21 21 ASP B 87 GLY B 102 1 16 HELIX 22 22 SER B 118 ALA B 132 1 15 HELIX 23 23 ILE B 142 VAL B 147 1 6 HELIX 24 24 THR B 151 ASP B 160 1 10 HELIX 25 25 SER B 172 LYS B 183 1 12 HELIX 26 26 GLU B 193 GLY B 195 5 3 HELIX 27 27 ASP B 196 GLY B 204 1 9 HELIX 28 28 ALA B 212 GLU B 229 1 18 HELIX 29 29 ASP B 231 PHE B 250 1 20 HELIX 30 30 PRO B 255 MET B 265 1 11 HELIX 31 31 PRO B 280 ASP B 293 1 14
SHEET 1 A 9 ILE A 11 ALA A 14 0 SHEET 2 A 9 GLY A 44 LEU A 47 1 O LEU A 46 N THR A 13 SHEET 3 A 9 LEU A 79 GLY A 82 1 O ILE A 80 N LEU A 47 SHEET 4 A 9 ALA A 106 ILE A 110 1 O LEU A 108 N ALA A 81 SHEET 5 A 9 ILE A 137 ASN A 141 1 O ILE A 138 N GLY A 107 SHEET 6 A 9 ILE A 164 GLU A 169 1 O LYS A 168 N ILE A 139 SHEET 7 A 9 LEU A 188 THR A 191 1 O TYR A 190 N GLU A 169 SHEET 8 A 9 GLY A 207 SER A 210 1 O ILE A 209 N THR A 191 SHEET 9 A 9 ILE A 11 ALA A 14 1 N ILE A 12 O SER A 210 SHEET 1 B 9 ILE B 11 ALA B 14 0 SHEET 2 B 9 GLY B 44 LEU B 47 1 O LEU B 46 N THR B 13 SHEET 3 B 9 LEU B 79 GLY B 82 1 O ILE B 80 N LEU B 47 SHEET 4 B 9 ALA B 106 ILE B 110 1 O LEU B 108 N ALA B 81 SHEET 5 B 9 ILE B 137 ASN B 141 1 O ILE B 138 N GLY B 107 SHEET 6 B 9 ILE B 164 GLU B 169 1 O LYS B 168 N ILE B 139 SHEET 7 B 9 LEU B 188 THR B 191 1 O LEU B 188 N ILE B 165 SHEET 8 B 9 GLY B 207 SER B 210 1 O ILE B 209 N THR B 191 SHEET 9 B 9 ILE B 11 ALA B 14 1 N ALA B 14 O SER B 210
LINK O ILE B 164 K K B 401 1555 1555 2.35 LINK OE2 GLU A 62 K K A 402 1555 1555 2.42 LINK O HIS A 161 K K A 401 1555 1555 2.47 LINK O ILE A 164 K K A 401 1555 1555 2.47 LINK O SER A 54 K K A 402 1555 1555 2.47 LINK O LEU B 57 K K B 402 1555 1555 2.47 LINK K K B 402 O HOH B 572 1555 1555 2.48 LINK O ALA A 159 K K A 401 1555 1555 2.48 LINK O ALA B 159 K K B 401 1555 1555 2.48 LINK O LEU A 57 K K A 402 1555 1555 2.55 LINK O HIS B 161 K K B 401 1555 1555 2.62 LINK O SER B 54 K K B 402 1555 1555 2.64 LINK OE2 GLU B 62 K K B 402 1555 1555 2.74
CISPEP 1 SER A 254 PRO A 255 0 13.55 CISPEP 2 LEU A 274 PRO A 275 0 12.69 CISPEP 3 SER B 254 PRO B 255 0 16.02 CISPEP 4 LEU B 274 PRO B 275 0 19.29
SITE 1 AC1 3 ALA A 159 HIS A 161 ILE A 164 SITE 1 AC2 3 SER A 54 LEU A 57 GLU A 62 SITE 1 AC3 12 ALA A 14 LEU A 46 GLY A 49 THR A 50 SITE 2 AC3 12 THR A 51 TYR A 140 LYS A 168 ILE A 209 SITE 3 AC3 12 GOL A 404 MES A 406 HOH A 619 TYR B 114 SITE 1 AC4 10 ALA A 48 GLY A 49 THR A 50 SER A 54 SITE 2 AC4 10 GLY A 84 LEU A 108 ALA A 109 ILE A 110 SITE 3 AC4 10 GOL A 403 TYR B 114 SITE 1 AC5 8 THR A 56 ARG A 273 LEU A 274 LEU A 307 SITE 2 AC5 8 ARG A 308 ASP B 87 THR B 88 ARG B 89 SITE 1 AC6 9 TYR A 140 ILE A 142 ARG A 145 GLY A 192 SITE 2 AC6 9 GLU A 193 PHE A 250 GOL A 403 HOH A 606 SITE 3 AC6 9 HOH A 619 SITE 1 AC7 3 ALA B 159 HIS B 161 ILE B 164 SITE 1 AC8 4 SER B 54 LEU B 57 GLU B 62 HOH B 572 SITE 1 AC9 12 TYR A 114 ALA B 14 LEU B 46 GLY B 49 SITE 2 AC9 12 THR B 50 THR B 51 LEU B 108 TYR B 140 SITE 3 AC9 12 LYS B 168 MES B 404 HOH B 528 HOH B 542 SITE 1 BC1 8 THR B 51 TYR B 140 ARG B 145 GLU B 193 SITE 2 BC1 8 PHE B 250 GOL B 403 HOH B 566 HOH B 604
CRYST1 62.357 105.332 105.510 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 0.016037 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009494 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009478 0.00000