10 20 30 40 50 60 70 80 1YXD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 20-FEB-05 1YXD
TITLE STRUCTURE OF E. COLI DIHYDRODIPICOLINATE SYNTHASE BOUND TITLE 2 WITH ALLOSTERIC INHIBITOR (S)-LYSINE TO 2.0 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 2 24-FEB-09 1YXD 1 VERSN REVDAT 1 02-AUG-05 1YXD 0
JRNL AUTH R.C.DOBSON,M.D.GRIFFIN,G.B.JAMESON,J.A.GERRARD JRNL TITL THE CRYSTAL STRUCTURES OF NATIVE AND JRNL TITL 2 (S)-LYSINE-BOUND DIHYDRODIPICOLINATE SYNTHASE FROM JRNL TITL 3 ESCHERICHIA COLI WITH IMPROVED RESOLUTION SHOW NEW JRNL TITL 4 FEATURES OF BIOLOGICAL 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 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 60077 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3225 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4393 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4321 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 557 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : 0.27000 REMARK 3 B12 (A**2) : -0.09000 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): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.581 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4418 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4159 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6008 ; 1.531 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9635 ; 0.901 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 582 ; 6.125 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;34.849 ;24.512 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 721 ;15.372 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.089 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 732 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4929 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 804 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 923 ; 0.233 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4056 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2226 ; 0.168 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2288 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 462 ; 0.147 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 6 ; 0.163 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.173 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 44 ; 0.252 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.272 ; 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): 2914 ; 0.700 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1204 ; 0.179 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4694 ; 1.307 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1514 ; 2.357 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1314 ; 3.779 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 1YXD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-05. REMARK 100 THE RCSB ID CODE IS RCSB032031.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 10 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : 63306 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 37.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.880 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.35600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.100 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: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M POTASSIUM PHOSPHATE, PH 10, REMARK 280 VAPOR 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 36.69467 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 73.38933 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 73.38933 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 36.69467 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 36.69467
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 LYS A 153 NZ REMARK 470 LYS A 155 CD CE NZ REMARK 470 GLU A 175 CD OE1 OE2 REMARK 470 ASP A 179 CG OD1 OD2 REMARK 470 ARG A 212 CD NE CZ NH1 NH2 REMARK 470 LYS A 257 NZ REMARK 470 ARG A 279 NE CZ NH1 NH2 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 ARG B 91 CD NE CZ NH1 NH2 REMARK 470 LYS B 153 NZ REMARK 470 LYS B 155 CD CE NZ REMARK 470 ASP B 179 OD1 OD2 REMARK 470 LYS B 257 CE NZ 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 REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1385 O HOH A 1385 6555 1.68 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 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 187 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP B 187 CB - CG - OD2 ANGL. DEV. = 6.8 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 TYR A 107 -48.93 81.86 REMARK 500 VAL A 135 70.79 -153.38 REMARK 500 TYR B 107 -48.89 80.55 REMARK 500 VAL B 135 71.83 -151.80 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 A1301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 154 O REMARK 620 2 LYS A 155 O 67.5 REMARK 620 3 ILE A 157 O 84.5 97.7 REMARK 620 4 ALA A 152 O 81.3 145.4 93.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B2301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE B 157 O REMARK 620 2 LYS B 155 O 94.3 REMARK 620 3 HOH B3498 O 167.4 88.4 REMARK 620 4 HOH B3584 O 96.3 123.4 92.4 REMARK 620 5 ALA B 152 O 96.5 146.3 74.8 87.0 REMARK 620 6 VAL B 154 O 80.3 68.0 89.4 168.5 82.5 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 1301 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1302 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 2301 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 2302 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS B 1300 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS B 2300 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS B 3301
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 CRYSTAL STRUCTURE ANALYSIS OF A MUTANT OF REMARK 900 DIHYDRODIPICOLINATE SYNTHASE--RESIDUE THR44 TO VAL44 REMARK 900 RELATED ID: 1S5V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF A MUTANT OF REMARK 900 DIHYDRODIPICOLINATE SYNTHASE--RESIDUE TYR107 TO PHE107 REMARK 900 RELATED ID: 1S5W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF A MUTANT OF REMARK 900 DIHYDRODIPICOLINATE SYNTHASE--RESIDUE TYR133 TO PHE133 REMARK 900 RELATED ID: 1YXC RELATED DB: PDB REMARK 900 DIHYDRODIPICOLINATE SYNTHASE TO 1.9 A
DBREF 1YXD A 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 DBREF 1YXD 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 A1301 1 HET CL A1302 1 HET K B2301 1 HET CL B2302 1 HET LYS B1300 10 HET LYS B2300 10 HET LYS B3301 10
HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM LYS LYSINE
FORMUL 3 K 2(K 1+) FORMUL 4 CL 2(CL 1-) FORMUL 7 LYS 3(C6 H15 N2 O2 1+) FORMUL 9 HOH *557(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 ASN A 93 1 13 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 LYS A 153 1 10 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 ASN B 93 1 13 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 ALA B 152 1 9 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 ILE A 39 SHEET 4 A 9 GLY A 99 VAL A 103 1 O LEU A 101 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 GLU A 162 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 ALA A 8 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 K K A1301 O VAL A 154 1555 1555 2.60 LINK K K A1301 O LYS A 155 1555 1555 3.06 LINK K K A1301 O ILE A 157 1555 1555 2.65 LINK K K A1301 O ALA A 152 1555 1555 2.66 LINK K K B2301 O ILE B 157 1555 1555 2.62 LINK K K B2301 O LYS B 155 1555 1555 3.16 LINK K K B2301 O HOH B3498 1555 1555 2.84 LINK K K B2301 O HOH B3584 1555 1555 3.03 LINK K K B2301 O ALA B 152 1555 1555 2.59 LINK K K B2301 O VAL B 154 1555 1555 2.67
CISPEP 1 ASN A 248 PRO A 249 0 5.85 CISPEP 2 LEU A 269 PRO A 270 0 11.16 CISPEP 3 ASN B 248 PRO B 249 0 6.27 CISPEP 4 LEU B 269 PRO B 270 0 11.74
SITE 1 AC1 4 ALA A 152 VAL A 154 LYS A 155 ILE A 157 SITE 1 AC2 6 GLY A 43 THR A 44 LEU A 101 LYS A 161 SITE 2 AC2 6 HOH A1345 HOH A1349 SITE 1 AC3 6 ALA B 152 VAL B 154 LYS B 155 ILE B 157 SITE 2 AC3 6 HOH B3498 HOH B3584 SITE 1 AC4 5 THR B 44 LEU B 101 LYS B 161 HOH B3342 SITE 2 AC4 5 HOH B3360 SITE 1 AC5 12 SER A 48 ALA A 49 LEU A 51 HIS A 53 SITE 2 AC5 12 HIS A 56 TYR A 106 HOH A1436 ASN B 80 SITE 3 AC5 12 GLU B 84 LYS B2300 HOH B3302 HOH B3304 SITE 1 AC6 10 ASN A 80 GLU A 84 SER B 48 ALA B 49 SITE 2 AC6 10 LEU B 51 HIS B 56 TYR B 106 LYS B1300 SITE 3 AC6 10 HOH B3375 HOH B3432 SITE 1 AC7 4 HOH A1482 ALA B 33 HOH B3305 HOH B3308
CRYST1 121.148 121.148 110.084 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 0.008254 0.004766 0.000000 0.00000
SCALE2 0.000000 0.009531 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009084 0.00000