HEADER LYASE 20-FEB-05 1YXC
TITLE STRUCTURE OF E. COLI DIHYDRODIPICOLINATE SYNTHASE TO 1.9 A
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: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: DAPA;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBLUESCRIPT +KS
KEYWDS DIHYDRODIPICOLINATE SYNTHASE, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.C.J.DOBSON,M.D.W.GRIFFIN,G.B.JAMESON,J.A.GERRARD
REVDAT 4 25-OCT-23 1YXC 1 REMARK LINK
REVDAT 3 11-OCT-17 1YXC 1 REMARK
REVDAT 2 24-FEB-09 1YXC 1 VERSN
REVDAT 1 02-AUG-05 1YXC 0
JRNL AUTH R.C.DOBSON,M.D.GRIFFIN,G.B.JAMESON,J.A.GERRARD
JRNL TITL THE CRYSTAL STRUCTURES OF NATIVE AND (S)-LYSINE-BOUND
JRNL TITL 2 DIHYDRODIPICOLINATE SYNTHASE FROM ESCHERICHIA COLI WITH
JRNL TITL 3 IMPROVED RESOLUTION SHOW NEW FEATURES OF BIOLOGICAL
JRNL TITL 4 SIGNIFICANCE.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1116 2005
JRNL REFN ISSN 0907-4449
JRNL PMID 16041077
JRNL DOI 10.1107/S0907444905016318
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0003
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) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.56
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 69522
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) : 0.174
REMARK 3 R VALUE (WORKING SET) : 0.172
REMARK 3 FREE R VALUE : 0.211
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 3700
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) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5195
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2660
REMARK 3 BIN FREE R VALUE SET COUNT : 185
REMARK 3 BIN FREE R VALUE : 0.3480
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4304
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 4
REMARK 3 SOLVENT ATOMS : 616
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.92
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.11000
REMARK 3 B22 (A**2) : -0.11000
REMARK 3 B33 (A**2) : 0.17000
REMARK 3 B12 (A**2) : -0.06000
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): 0.104
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.741
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4374 ; 0.015 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 4117 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5957 ; 1.570 ; 1.951
REMARK 3 BOND ANGLES OTHERS (DEGREES): 9520 ; 0.901 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 582 ; 6.439 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;35.585 ;24.250
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 711 ;15.108 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.511 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 729 ; 0.102 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4902 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 808 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 956 ; 0.232 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4148 ; 0.187 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2207 ; 0.171 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 2286 ; 0.094 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 457 ; 0.160 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.124 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 10 ; 0.199 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 55 ; 0.233 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.159 ; 0.200
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): 2899 ; 0.754 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1192 ; 0.209 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4669 ; 1.343 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1485 ; 2.381 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1288 ; 3.885 ; 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 : 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 ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 1YXC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-05.
REMARK 100 THE DEPOSITION ID IS D_1000032030.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 31-AUG-04
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : 10
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200 DATA SCALING SOFTWARE : D*TREK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73225
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 39.570
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 4.300
REMARK 200 R MERGE (I) : 0.08900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 4.17
REMARK 200 R MERGE FOR SHELL (I) : 0.35800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: 1DHP
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 66.86
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M POTASSIUM PHOSPHATE, PH 10, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 276K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.73133
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.46267
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.46267
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.73133
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 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 -0.500000 -0.866025 0.000000 0.00000
REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 36.73133
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 MET A 1 CB CG SD CE
REMARK 470 MET A 61 CE
REMARK 470 ASP A 94 CG OD1 OD2
REMARK 470 GLU A 146 CD OE1 OE2
REMARK 470 LYS A 155 CD CE NZ
REMARK 470 ASP A 179 CG OD1 OD2
REMARK 470 ARG A 212 CD NE CZ NH1 NH2
REMARK 470 GLN A 216 CG CD OE1 NE2
REMARK 470 LYS A 219 CE NZ
REMARK 470 GLU A 228 CG CD OE1 OE2
REMARK 470 LYS A 257 CE NZ
REMARK 470 GLU A 280 CG CD OE1 OE2
REMARK 470 LYS A 287 CD CE NZ
REMARK 470 GLU B 15 CD OE1 OE2
REMARK 470 LYS B 16 CE NZ
REMARK 470 MET B 61 CE
REMARK 470 ASP B 94 CG OD1 OD2
REMARK 470 GLU B 124 CD OE1 OE2
REMARK 470 GLU B 146 CD OE1 OE2
REMARK 470 LYS B 153 CE NZ
REMARK 470 LYS B 155 CD CE NZ
REMARK 470 ASP B 179 CG OD1 OD2
REMARK 470 LYS B 257 CE NZ
REMARK 470 ARG B 279 NE CZ NH1 NH2
REMARK 470 GLU B 280 CG CD OE1 OE2
REMARK 470 LYS B 287 CE NZ
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 OG1 THR A 272 O HOH A 1365 1.98
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 187 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES
REMARK 500 ASP A 276 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES
REMARK 500 ARG B 109 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 ARG B 109 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 ASP B 187 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES
REMARK 500 ARG B 230 NE - CZ - NH2 ANGL. DEV. = 3.2 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 PHE A 2 46.02 -143.10
REMARK 500 TYR A 107 -50.39 74.73
REMARK 500 ALA A 210 48.64 -143.43
REMARK 500 TYR B 107 -47.52 78.12
REMARK 500 VAL B 135 73.20 -151.79
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 K A1300 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 152 O
REMARK 620 2 VAL A 154 O 82.4
REMARK 620 3 LYS A 155 O 147.0 66.9
REMARK 620 4 ILE A 157 O 92.9 81.4 94.2
REMARK 620 5 HOH A1464 O 77.4 92.1 91.3 169.0
REMARK 620 6 HOH A1550 O 89.5 165.5 123.0 87.0 97.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 K B2300 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA B 152 O
REMARK 620 2 VAL B 154 O 81.9
REMARK 620 3 LYS B 155 O 145.8 66.7
REMARK 620 4 ILE B 157 O 94.4 78.7 92.4
REMARK 620 5 HOH B2508 O 80.3 93.7 88.3 171.3
REMARK 620 6 HOH B2543 O 95.1 175.8 116.9 98.8 88.6
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 K A 1300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 2300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 2301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1DHP RELATED DB: PDB
REMARK 900 FIRST STRUCTURE OF DIHYRODIPICOLINATE SYNTHASE
REMARK 900 RELATED ID: 1S5T RELATED DB: PDB
REMARK 900 A MUTANT OF DIHYDRODIPICOLINATE SYNTHASE--RESIDUE THR44 TO VAL44
REMARK 900 RELATED ID: 1S5V RELATED DB: PDB
REMARK 900 A MUTANT OF DIHYDRODIPICOLINATE SYNTHASE--RESIDUE TYR107 TO PHE107
REMARK 900 RELATED ID: 1S5W RELATED DB: PDB
REMARK 900 A MUTANT OF DIHYDRODIPICOLINATE SYNTHASE--RESIDUE TYR133 TO PHE133
REMARK 900 RELATED ID: 1YXD RELATED DB: PDB
REMARK 900 DIHYDRODIPICOLINATE SYNTHASE BOUND WITH ALLOSTERIC INHIBITOR (S)-
REMARK 900 LYSINE TO 2.0 A
DBREF 1YXC A 1 292 UNP P0A6L2 DAPA_ECOLI 1 292
DBREF 1YXC B 1 292 UNP P0A6L2 DAPA_ECOLI 1 292
SEQRES 1 A 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET
SEQRES 2 A 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS
SEQRES 3 A 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE
SEQRES 4 A 292 VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU ASN
SEQRES 5 A 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP
SEQRES 6 A 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY
SEQRES 7 A 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG
SEQRES 8 A 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR
SEQRES 9 A 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN
SEQRES 10 A 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN
SEQRES 11 A 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU
SEQRES 12 A 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN
SEQRES 13 A 292 ILE ILE GLY ILE LYS GLU ALA THR GLY ASN LEU THR ARG
SEQRES 14 A 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL
SEQRES 15 A 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET
SEQRES 16 A 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN
SEQRES 17 A 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA
SEQRES 18 A 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN
SEQRES 19 A 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO
SEQRES 20 A 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY
SEQRES 21 A 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO
SEQRES 22 A 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU
SEQRES 23 A 292 LYS HIS ALA GLY LEU LEU
SEQRES 1 B 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET
SEQRES 2 B 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS
SEQRES 3 B 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE
SEQRES 4 B 292 VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU ASN
SEQRES 5 B 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP
SEQRES 6 B 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY
SEQRES 7 B 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG
SEQRES 8 B 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR
SEQRES 9 B 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN
SEQRES 10 B 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN
SEQRES 11 B 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU
SEQRES 12 B 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN
SEQRES 13 B 292 ILE ILE GLY ILE LYS GLU ALA THR GLY ASN LEU THR ARG
SEQRES 14 B 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL
SEQRES 15 B 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET
SEQRES 16 B 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN
SEQRES 17 B 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA
SEQRES 18 B 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN
SEQRES 19 B 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO
SEQRES 20 B 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY
SEQRES 21 B 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO
SEQRES 22 B 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU
SEQRES 23 B 292 LYS HIS ALA GLY LEU LEU
HET K A1300 1
HET CL A1301 1
HET K B2300 1
HET CL B2301 1
HETNAM K POTASSIUM ION
HETNAM CL CHLORIDE ION
FORMUL 3 K 2(K 1+)
FORMUL 4 CL 2(CL 1-)
FORMUL 7 HOH *616(H2 O)
HELIX 1 1 CYS A 20 GLY A 35 1 16
HELIX 2 2 GLU A 47 LEU A 51 5 5
HELIX 3 3 ASN A 52 ASP A 68 1 17
HELIX 4 4 ALA A 81 ARG A 91 1 11
HELIX 5 5 SER A 111 HIS A 125 1 15
HELIX 6 6 VAL A 135 GLY A 140 1 6
HELIX 7 7 LEU A 144 ALA A 152 1 9
HELIX 8 8 THR A 168 GLU A 175 1 8
HELIX 9 9 ASP A 187 ALA A 189 5 3
HELIX 10 10 SER A 190 LEU A 197 1 8
HELIX 11 11 VAL A 205 VAL A 209 5 5
HELIX 12 12 ALA A 210 GLU A 223 1 14
HELIX 13 13 HIS A 225 LEU A 243 1 19
HELIX 14 14 PRO A 249 LEU A 259 1 11
HELIX 15 15 THR A 275 ALA A 289 1 15
HELIX 16 16 CYS B 20 GLY B 35 1 16
HELIX 17 17 GLU B 47 LEU B 51 5 5
HELIX 18 18 ASN B 52 ASP B 68 1 17
HELIX 19 19 ALA B 81 ARG B 91 1 11
HELIX 20 20 SER B 111 HIS B 125 1 15
HELIX 21 21 VAL B 135 GLY B 140 1 6
HELIX 22 22 LEU B 144 LYS B 153 1 10
HELIX 23 23 THR B 168 GLU B 175 1 8
HELIX 24 24 ASP B 187 ALA B 189 5 3
HELIX 25 25 SER B 190 LEU B 197 1 8
HELIX 26 26 VAL B 205 VAL B 209 5 5
HELIX 27 27 ALA B 210 GLU B 223 1 14
HELIX 28 28 HIS B 225 LEU B 243 1 19
HELIX 29 29 PRO B 249 LEU B 259 1 11
HELIX 30 30 THR B 275 ALA B 289 1 15
SHEET 1 A 9 GLY A 4 ALA A 8 0
SHEET 2 A 9 ALA A 38 SER A 41 1 O VAL A 40 N VAL A 7
SHEET 3 A 9 VAL A 73 GLY A 76 1 O ILE A 74 N SER A 41
SHEET 4 A 9 GLY A 99 VAL A 103 1 O GLY A 99 N ALA A 75
SHEET 5 A 9 GLN A 130 ASN A 134 1 O ILE A 131 N CYS A 100
SHEET 6 A 9 ILE A 157 GLU A 162 1 O LYS A 161 N LEU A 132
SHEET 7 A 9 VAL A 182 SER A 185 1 O LEU A 184 N ILE A 160
SHEET 8 A 9 GLY A 201 SER A 204 1 O ILE A 203 N SER A 185
SHEET 9 A 9 GLY A 4 ALA A 8 1 N ILE A 6 O SER A 204
SHEET 1 B 9 GLY B 4 ALA B 8 0
SHEET 2 B 9 ALA B 38 SER B 41 1 O VAL B 40 N VAL B 7
SHEET 3 B 9 VAL B 73 GLY B 76 1 O ILE B 74 N ILE B 39
SHEET 4 B 9 GLY B 99 VAL B 103 1 O LEU B 101 N ALA B 75
SHEET 5 B 9 GLN B 130 ASN B 134 1 O ILE B 131 N CYS B 100
SHEET 6 B 9 ILE B 157 GLU B 162 1 O LYS B 161 N LEU B 132
SHEET 7 B 9 VAL B 182 SER B 185 1 O LEU B 184 N ILE B 160
SHEET 8 B 9 GLY B 201 SER B 204 1 O ILE B 203 N SER B 185
SHEET 9 B 9 GLY B 4 ALA B 8 1 N ILE B 6 O SER B 204
LINK O ALA A 152 K K A1300 1555 1555 2.75
LINK O VAL A 154 K K A1300 1555 1555 2.67
LINK O LYS A 155 K K A1300 1555 1555 3.10
LINK O ILE A 157 K K A1300 1555 1555 2.69
LINK K K A1300 O HOH A1464 1555 1555 2.82
LINK K K A1300 O HOH A1550 1555 1555 2.90
LINK O ALA B 152 K K B2300 1555 1555 2.62
LINK O VAL B 154 K K B2300 1555 1555 2.61
LINK O LYS B 155 K K B2300 1555 1555 3.25
LINK O ILE B 157 K K B2300 1555 1555 2.66
LINK K K B2300 O HOH B2508 1555 1555 2.74
LINK K K B2300 O HOH B2543 1555 1555 2.90
CISPEP 1 ASN A 248 PRO A 249 0 4.58
CISPEP 2 LEU A 269 PRO A 270 0 11.35
CISPEP 3 ASN B 248 PRO B 249 0 4.99
CISPEP 4 LEU B 269 PRO B 270 0 8.37
SITE 1 AC1 6 ALA A 152 VAL A 154 LYS A 155 ILE A 157
SITE 2 AC1 6 HOH A1464 HOH A1550
SITE 1 AC2 5 THR A 44 LEU A 101 LYS A 161 HOH A1331
SITE 2 AC2 5 HOH A1372
SITE 1 AC3 6 ALA B 152 VAL B 154 LYS B 155 ILE B 157
SITE 2 AC3 6 HOH B2508 HOH B2543
SITE 1 AC4 5 THR B 44 LEU B 101 LYS B 161 HOH B2330
SITE 2 AC4 5 HOH B2340
CRYST1 120.869 120.869 110.194 90.00 90.00 120.00 P 31 2 1 12
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 0.008273 0.004777 0.000000 0.00000
SCALE2 0.000000 0.009553 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009075 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
