HEADER LYASE 15-APR-12 4EOU
TITLE CRYSTAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE SYNTHASE WITH
TITLE 2 PYRUVATE AND SUCCINIC SEMI-ALDEHYDE BOUND IN ACTIVE SITE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: DHDPS;
COMPND 5 EC: 4.2.1.52
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 STRAIN: XL1-BLUE;
SOURCE 5 OTHER_DETAILS: HARBORING PLASMID PJG001
KEYWDS ALPHA/BETA BARREL, TIM BARREL, AMINO-ACID BIOSYNTHESIS, SCHIFF BASE,
KEYWDS 2 LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR B.A.BOUGHTON,R.C.J.DOBSON,C.A.HUTTON
REVDAT 5 06-DEC-23 4EOU 1 REMARK
REVDAT 4 13-SEP-23 4EOU 1 REMARK LINK
REVDAT 3 25-JUL-12 4EOU 1 JRNL
REVDAT 2 06-JUN-12 4EOU 1 JRNL
REVDAT 1 25-APR-12 4EOU 0
SPRSDE 25-APR-12 4EOU 3UBS
JRNL AUTH B.A.BOUGHTON,R.C.DOBSON,C.A.HUTTON
JRNL TITL THE CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM
JRNL TITL 2 ESCHERICHIA COLI WITH BOUND PYRUVATE AND SUCCINIC ACID
JRNL TITL 3 SEMIALDEHYDE: UNAMBIGUOUS RESOLUTION OF THE STEREOCHEMISTRY
JRNL TITL 4 OF THE CONDENSATION PRODUCT.
JRNL REF PROTEINS V. 80 2117 2012
JRNL REFN ISSN 0887-3585
JRNL PMID 22552955
JRNL DOI 10.1002/PROT.24106
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.6.0117
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 89.1
REMARK 3 NUMBER OF REFLECTIONS : 35072
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) : 0.146
REMARK 3 R VALUE (WORKING SET) : 0.143
REMARK 3 FREE R VALUE : 0.198
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.700
REMARK 3 FREE R VALUE TEST SET COUNT : 2110
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2550
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.79
REMARK 3 BIN R VALUE (WORKING SET) : 0.1570
REMARK 3 BIN FREE R VALUE SET COUNT : 51
REMARK 3 BIN FREE R VALUE : 0.2240
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4378
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 16
REMARK 3 SOLVENT ATOMS : 459
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.11
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.14000
REMARK 3 B22 (A**2) : -0.14000
REMARK 3 B33 (A**2) : 0.20000
REMARK 3 B12 (A**2) : -0.07000
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): 0.196
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.069
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4503 ; 0.019 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6129 ; 1.940 ; 1.977
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 594 ; 6.515 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;37.210 ;24.432
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 744 ;15.778 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.125 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 740 ; 0.123 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3351 ; 0.010 ; 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
REMARK 3 U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 4EOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-12.
REMARK 100 THE DEPOSITION ID IS D_1000071886.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-JUL-08
REMARK 200 TEMPERATURE (KELVIN) : 110
REMARK 200 PH : 10.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON
REMARK 200 BEAMLINE : MX2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.95364
REMARK 200 MONOCHROMATOR : YALE MIRRORS
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35072
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 29.100
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 89.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.10300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.32500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700
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 1YXC
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 66.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.69
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 6% W/V N-OCTYL-R-GLUCOPYRANOSIDE, 1.8
REMARK 280 M POTASSIUM PHOSPHATE DIBASIC, PH 10.0, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 277K
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 36.57733
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 73.15467
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 73.15467
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 36.57733
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: 10580 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 38830 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 73.15467
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 LYS A 16 NZ
REMARK 470 LYS A 25 NZ
REMARK 470 LYS A 120 NZ
REMARK 470 LYS A 155 CD CE NZ
REMARK 470 GLU A 175 OE1 OE2
REMARK 470 LYS A 257 NZ
REMARK 470 LYS B 25 NZ
REMARK 470 ASP B 94 CG OD1 OD2
REMARK 470 LYS B 155 CD CE NZ
REMARK 470 ARG B 212 CD NE CZ NH1 NH2
REMARK 470 LYS B 219 CE NZ
REMARK 470 LYS B 257 NZ
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 N MET B 1 O HOH B 508 2.00
REMARK 500 N MET A 1 O HOH A 508 2.02
REMARK 500
REMARK 500 REMARK: NULL
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 118 CG HIS A 118 CD2 0.062
REMARK 500 HIS B 53 CG HIS B 53 CD2 0.065
REMARK 500 HIS B 240 CG HIS B 240 CD2 0.067
REMARK 500 HIS B 288 CG HIS B 288 CD2 0.070
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 LEU A 183 CB - CG - CD2 ANGL. DEV. = -10.6 DEGREES
REMARK 500 ARG B 235 NE - CZ - NH1 ANGL. DEV. = 3.0 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 -50.90 81.40
REMARK 500 TYR B 107 -54.78 78.08
REMARK 500 PRO B 249 31.20 -99.65
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 A 303 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 123 O
REMARK 620 2 GLU A 124 O 67.9
REMARK 620 3 THR A 126 O 70.3 88.3
REMARK 620 4 HOH A 512 O 64.6 96.8 128.3
REMARK 620 5 HOH A 557 O 116.2 69.2 149.7 76.3
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 K A 301 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 152 O
REMARK 620 2 VAL A 154 O 85.6
REMARK 620 3 LYS A 155 O 145.6 63.8
REMARK 620 4 ILE A 157 O 101.8 85.8 91.6
REMARK 620 5 HOH A 514 O 79.9 96.1 87.8 177.5
REMARK 620 6 HOH A 568 O 93.8 175.8 115.6 98.4 79.7
REMARK 620 7 HOH A 588 O 138.9 130.8 67.2 99.7 77.9 48.4
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 K B 303 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA B 123 O
REMARK 620 2 THR B 126 O 72.5
REMARK 620 3 HOH B 500 O 68.0 133.5
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 K B 301 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 142.6 64.1
REMARK 620 4 ILE B 157 O 99.9 82.9 91.3
REMARK 620 5 HOH B 561 O 75.8 88.5 87.7 170.9
REMARK 620 6 HOH B 603 O 146.1 109.9 48.7 112.8 72.9
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 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 303
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1YXC RELATED DB: PDB
REMARK 900 RELATED ID: 3DU0 RELATED DB: PDB
REMARK 900 RELATED ID: 1DHP RELATED DB: PDB
DBREF 4EOU A 1 292 UNP P0A6L2 DAPA_ECOLI 1 292
DBREF 4EOU 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 LYF 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 LYF 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
MODRES 4EOU LYF A 161 LYS
MODRES 4EOU LYF B 161 LYS
HET LYF A 161 21
HET LYF B 161 21
HET K A 301 1
HET GOL A 302 6
HET K A 303 1
HET K B 301 1
HET GOL B 302 6
HET K B 303 1
HETNAM LYF (2E,4S)-2-{[(5S)-5-AMINO-5-CARBOXYPENTYL]IMINO}-4-
HETNAM 2 LYF HYDROXYHEPTANEDIOIC ACID
HETNAM K POTASSIUM ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 LYF 2(C13 H22 N2 O7)
FORMUL 3 K 4(K 1+)
FORMUL 4 GOL 2(C3 H8 O3)
FORMUL 9 HOH *459(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 PHE A 92 1 12
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 LEU A 197 1 11
HELIX 10 10 VAL A 205 VAL A 209 5 5
HELIX 11 11 ALA A 210 GLU A 223 1 14
HELIX 12 12 HIS A 225 LEU A 243 1 19
HELIX 13 13 PRO A 249 LEU A 259 1 11
HELIX 14 14 THR A 275 ALA A 289 1 15
HELIX 15 15 CYS B 20 GLY B 35 1 16
HELIX 16 16 GLU B 47 LEU B 51 5 5
HELIX 17 17 ASN B 52 ASP B 68 1 17
HELIX 18 18 ALA B 81 ARG B 91 1 11
HELIX 19 19 SER B 111 HIS B 125 1 15
HELIX 20 20 VAL B 135 GLY B 140 1 6
HELIX 21 21 LEU B 144 ALA B 152 1 9
HELIX 22 22 THR B 168 GLU B 175 1 8
HELIX 23 23 ASP B 187 LEU B 197 1 11
HELIX 24 24 VAL B 205 VAL B 209 5 5
HELIX 25 25 ALA B 210 GLU B 223 1 14
HELIX 26 26 HIS B 225 LEU B 243 1 19
HELIX 27 27 PRO B 249 LEU B 259 1 11
HELIX 28 28 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 LEU A 101 N ALA A 75
SHEET 5 A 9 GLN A 130 ASN A 134 1 O ILE A 131 N THR A 102
SHEET 6 A 9 ILE A 157 GLU A 162 1 O LYF 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 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 LYF B 161 N LEU B 132
SHEET 7 B 9 VAL B 182 SER B 185 1 O LEU B 184 N GLU B 162
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 C ILE A 160 N LYF A 161 1555 1555 1.33
LINK C LYF A 161 N GLU A 162 1555 1555 1.33
LINK C ILE B 160 N LYF B 161 1555 1555 1.35
LINK C LYF B 161 N GLU B 162 1555 1555 1.34
LINK O ALA A 123 K K A 303 1555 1555 2.92
LINK O GLU A 124 K K A 303 1555 1555 3.22
LINK O THR A 126 K K A 303 1555 1555 2.70
LINK O ALA A 152 K K A 301 1555 1555 2.69
LINK O VAL A 154 K K A 301 1555 1555 2.64
LINK O LYS A 155 K K A 301 1555 1555 3.25
LINK O ILE A 157 K K A 301 1555 1555 2.63
LINK K K A 301 O HOH A 514 1555 1555 2.84
LINK K K A 301 O HOH A 568 1555 1555 2.70
LINK K K A 301 O HOH A 588 1555 1555 3.22
LINK K K A 303 O HOH A 512 1555 1555 2.85
LINK K K A 303 O HOH A 557 1555 1555 3.15
LINK O ALA B 123 K K B 303 1555 1555 2.82
LINK O THR B 126 K K B 303 1555 1555 2.59
LINK O ALA B 152 K K B 301 1555 1555 2.75
LINK O VAL B 154 K K B 301 1555 1555 2.68
LINK O LYS B 155 K K B 301 1555 1555 3.27
LINK O ILE B 157 K K B 301 1555 1555 2.64
LINK K K B 301 O HOH B 561 1555 1555 3.01
LINK K K B 301 O HOH B 603 1555 1555 3.44
LINK K K B 303 O HOH B 500 1555 1555 2.88
CISPEP 1 ASN A 248 PRO A 249 0 8.61
CISPEP 2 LEU A 269 PRO A 270 0 13.01
CISPEP 3 ASN B 248 PRO B 249 0 3.10
CISPEP 4 LEU B 269 PRO B 270 0 13.62
SITE 1 AC1 6 ALA A 152 VAL A 154 LYS A 155 ILE A 157
SITE 2 AC1 6 HOH A 514 HOH A 568
SITE 1 AC2 7 SER A 48 ALA A 49 TYR A 106 HOH A 462
SITE 2 AC2 7 HOH A 585 ASN B 80 TYR B 107
SITE 1 AC3 4 ALA A 123 GLU A 124 THR A 126 HOH A 512
SITE 1 AC4 5 ALA B 152 VAL B 154 LYS B 155 ILE B 157
SITE 2 AC4 5 HOH B 561
SITE 1 AC5 9 ASN A 80 SER B 48 ALA B 49 GLY B 78
SITE 2 AC5 9 VAL B 103 TYR B 106 HOH B 411 HOH B 431
SITE 3 AC5 9 HOH B 547
SITE 1 AC6 3 ALA B 123 THR B 126 HOH B 500
CRYST1 121.172 121.172 109.732 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 0.008253 0.004765 0.000000 0.00000
SCALE2 0.000000 0.009529 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009113 0.00000
(ATOM LINES ARE NOT SHOWN.)
END