HEADER TRANSFERASE 08-JUL-10 3NVS
TITLE 1.02 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 3-PHOSPHOSHIKIMATE 1-
TITLE 2 CARBOXYVINYLTRANSFERASE FROM VIBRIO CHOLERAE IN COMPLEX WITH
TITLE 3 SHIKIMATE-3-PHOSPHATE (PARTIALLY PHOTOLYZED) AND GLYPHOSATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE, EPSP SYNTHASE,
COMPND 5 EPSPS;
COMPND 6 EC: 2.5.1.19;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE;
SOURCE 3 ORGANISM_TAXID: 666;
SOURCE 4 STRAIN: N16961;
SOURCE 5 GENE: AROA, NP_231368, VC_1732;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-DE3 (MAGIC);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7
KEYWDS STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS
KEYWDS 2 DISEASES, CSGID, INSIDE-OUT ALPHA-BETA BARREL, EPSP SYNTHASE,
KEYWDS 3 TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.MINASOV,S.H.LIGHT,A.HALAVATY,G.SHUVALOVA,L.PAPAZISI,W.F.ANDERSON,
AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID)
REVDAT 3 06-SEP-23 3NVS 1 REMARK SEQADV LINK
REVDAT 2 08-NOV-17 3NVS 1 REMARK
REVDAT 1 21-JUL-10 3NVS 0
JRNL AUTH G.MINASOV,S.H.LIGHT,A.HALAVATY,G.SHUVALOVA,L.PAPAZISI,
JRNL AUTH 2 W.F.ANDERSON,
JRNL AUTH 3 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES
JRNL AUTH 4 (CSGID)
JRNL TITL 1.02 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF
JRNL TITL 2 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE FROM VIBRIO
JRNL TITL 3 CHOLERAE IN COMPLEX WITH SHIKIMATE-3-PHOSPHATE (PARTIALLY
JRNL TITL 4 PHOTOLYZED) AND GLYPHOSATE
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.02 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
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) : 1.02
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.89
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 3 NUMBER OF REFLECTIONS : 169410
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) : 0.115
REMARK 3 R VALUE (WORKING SET) : 0.114
REMARK 3 FREE R VALUE : 0.138
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 8975
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) : 1.02
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.05
REMARK 3 REFLECTION IN BIN (WORKING SET) : 12205
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.35
REMARK 3 BIN R VALUE (WORKING SET) : 0.2130
REMARK 3 BIN FREE R VALUE SET COUNT : 620
REMARK 3 BIN FREE R VALUE : 0.2350
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3240
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 65
REMARK 3 SOLVENT ATOMS : 747
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 6.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.51
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.39000
REMARK 3 B22 (A**2) : 0.20000
REMARK 3 B33 (A**2) : 0.08000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.21000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.022
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.024
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.012
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.524
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.980
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3787 ; 0.011 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2503 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5191 ; 1.542 ; 1.987
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6186 ; 0.979 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 507 ; 5.421 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;36.345 ;25.183
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 653 ;10.672 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.118 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 584 ; 0.099 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4403 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 735 ; 0.003 ; 0.020
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): 2379 ; 1.687 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 961 ; 2.137 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3877 ; 2.363 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1408 ; 3.523 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1313 ; 5.008 ; 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): 3786 ; 1.808 ; 3.000
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 3NVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-10.
REMARK 100 THE DEPOSITION ID IS D_1000060340.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 14-JUN-10
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.82648
REMARK 200 MONOCHROMATOR : SI {1,1,1}
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 178530
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020
REMARK 200 RESOLUTION RANGE LOW (A) : 15.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 200 DATA REDUNDANCY : 2.200
REMARK 200 R MERGE (I) : 0.04400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5
REMARK 200 DATA REDUNDANCY IN SHELL : 2.20
REMARK 200 R MERGE FOR SHELL (I) : 0.39100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200
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 1G6S
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.02
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 4.0 MGR/ML, 0.25M SODIUM
REMARK 280 CLORIDE, 0.01M TRIS-HCL (PH 8.3), 2MM GLYPHOSATE, 1MM SHIKIMATE-
REMARK 280 3-PHOSPHATE; SCREEN: CLASSICS II (G12), 0.2M MAGNESIUM CHLORIDE,
REMARK 280 0.1M HEPES (PH 7.5), 25% (W/V) PEG3350., VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 43.74200
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 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 -23
REMARK 465 HIS A -22
REMARK 465 HIS A -21
REMARK 465 HIS A -20
REMARK 465 HIS A -19
REMARK 465 HIS A -18
REMARK 465 HIS A -17
REMARK 465 SER A -16
REMARK 465 SER A -15
REMARK 465 GLY A -14
REMARK 465 VAL A -13
REMARK 465 ASP A -12
REMARK 465 LEU A -11
REMARK 465 GLY A -10
REMARK 465 THR A -9
REMARK 465 GLU A -8
REMARK 465 ASN A -7
REMARK 465 LEU A -6
REMARK 465 TYR A -5
REMARK 465 PHE A -4
REMARK 465 GLN A -3
REMARK 465 SER A -2
REMARK 465 ASN A -1
REMARK 465 ALA A 0
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 40 NE - CZ - NH2 ANGL. DEV. = 3.1 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 GLU A 144 -104.44 -124.53
REMARK 500 GLU A 144 -51.97 -127.23
REMARK 500 ASN A 147 7.70 84.78
REMARK 500 TYR A 221 14.91 59.32
REMARK 500 TYR A 221 14.91 59.18
REMARK 500 LYS A 341 -145.94 -104.10
REMARK 500 SER A 398 -166.86 -174.06
REMARK 500 PHE A 414 69.04 -160.53
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 MG A 430 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 123 OE1
REMARK 620 2 GLN A 145 OE1 175.5
REMARK 620 3 HOH A 871 O 92.5 83.3
REMARK 620 4 HOH A 901 O 84.5 97.4 96.3
REMARK 620 5 HOH A 927 O 85.9 92.8 92.1 167.5
REMARK 620 6 HOH A1041 O 89.8 94.4 177.7 84.1 87.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 431 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 608 O
REMARK 620 2 HOH A 732 O 173.2
REMARK 620 3 HOH A 733 O 82.3 92.1
REMARK 620 4 HOH A 734 O 86.2 99.6 168.0
REMARK 620 5 HOH A 735 O 93.4 91.0 96.0 81.4
REMARK 620 6 HOH A1102 O 85.9 90.2 89.6 92.8 174.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 432 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 533 O
REMARK 620 2 HOH A 740 O 85.2
REMARK 620 3 HOH A 741 O 94.9 86.0
REMARK 620 4 HOH A 742 O 85.7 170.9 95.1
REMARK 620 5 HOH A 743 O 174.5 92.0 89.6 97.0
REMARK 620 6 HOH A 744 O 90.6 87.7 171.2 92.1 84.5
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 S3P A 427
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SKM A 428
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GPJ A 429
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 430
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 431
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 432
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 433
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 434
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 435
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 436
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 437
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 438
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: IDP90626 RELATED DB: TARGETDB
DBREF 3NVS A 1 426 UNP Q9KRB0 AROA_VIBCH 1 426
SEQADV 3NVS MET A -23 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS HIS A -22 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS HIS A -21 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS HIS A -20 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS HIS A -19 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS HIS A -18 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS HIS A -17 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS SER A -16 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS SER A -15 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS GLY A -14 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS VAL A -13 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS ASP A -12 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS LEU A -11 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS GLY A -10 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS THR A -9 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS GLU A -8 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS ASN A -7 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS LEU A -6 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS TYR A -5 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS PHE A -4 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS GLN A -3 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS SER A -2 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS ASN A -1 UNP Q9KRB0 EXPRESSION TAG
SEQADV 3NVS ALA A 0 UNP Q9KRB0 EXPRESSION TAG
SEQRES 1 A 450 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU
SEQRES 2 A 450 GLY THR GLU ASN LEU TYR PHE GLN SER ASN ALA MET GLU
SEQRES 3 A 450 SER LEU THR LEU GLN PRO ILE GLU LEU ILE SER GLY GLU
SEQRES 4 A 450 VAL ASN LEU PRO GLY SER LYS SER VAL SER ASN ARG ALA
SEQRES 5 A 450 LEU LEU LEU ALA ALA LEU ALA SER GLY THR THR ARG LEU
SEQRES 6 A 450 THR ASN LEU LEU ASP SER ASP ASP ILE ARG HIS MET LEU
SEQRES 7 A 450 ASN ALA LEU THR LYS LEU GLY VAL ASN TYR ARG LEU SER
SEQRES 8 A 450 ALA ASP LYS THR THR CYS GLU VAL GLU GLY LEU GLY GLN
SEQRES 9 A 450 ALA PHE HIS THR THR GLN PRO LEU GLU LEU PHE LEU GLY
SEQRES 10 A 450 ASN ALA GLY THR ALA MET ARG PRO LEU ALA ALA ALA LEU
SEQRES 11 A 450 CYS LEU GLY GLN GLY ASP TYR VAL LEU THR GLY GLU PRO
SEQRES 12 A 450 ARG MET LYS GLU ARG PRO ILE GLY HIS LEU VAL ASP ALA
SEQRES 13 A 450 LEU ARG GLN ALA GLY ALA GLN ILE GLU TYR LEU GLU GLN
SEQRES 14 A 450 GLU ASN PHE PRO PRO LEU ARG ILE GLN GLY THR GLY LEU
SEQRES 15 A 450 GLN ALA GLY THR VAL THR ILE ASP GLY SER ILE SER SER
SEQRES 16 A 450 GLN PHE LEU THR ALA PHE LEU MET SER ALA PRO LEU ALA
SEQRES 17 A 450 GLN GLY LYS VAL THR ILE LYS ILE VAL GLY GLU LEU VAL
SEQRES 18 A 450 SER LYS PRO TYR ILE ASP ILE THR LEU HIS ILE MET GLU
SEQRES 19 A 450 GLN PHE GLY VAL GLN VAL ILE ASN HIS ASP TYR GLN GLU
SEQRES 20 A 450 PHE VAL ILE PRO ALA GLY GLN SER TYR VAL SER PRO GLY
SEQRES 21 A 450 GLN PHE LEU VAL GLU GLY ASP ALA SER SER ALA SER TYR
SEQRES 22 A 450 PHE LEU ALA ALA ALA ALA ILE LYS GLY GLY GLU VAL LYS
SEQRES 23 A 450 VAL THR GLY ILE GLY LYS ASN SER ILE GLN GLY ASP ILE
SEQRES 24 A 450 GLN PHE ALA ASP ALA LEU GLU LYS MET GLY ALA GLN ILE
SEQRES 25 A 450 GLU TRP GLY ASP ASP TYR VAL ILE ALA ARG ARG GLY GLU
SEQRES 26 A 450 LEU ASN ALA VAL ASP LEU ASP PHE ASN HIS ILE PRO ASP
SEQRES 27 A 450 ALA ALA MET THR ILE ALA THR THR ALA LEU PHE ALA LYS
SEQRES 28 A 450 GLY THR THR ALA ILE ARG ASN VAL TYR ASN TRP ARG VAL
SEQRES 29 A 450 LYS GLU THR ASP ARG LEU ALA ALA MET ALA THR GLU LEU
SEQRES 30 A 450 ARG LYS VAL GLY ALA THR VAL GLU GLU GLY GLU ASP PHE
SEQRES 31 A 450 ILE VAL ILE THR PRO PRO THR LYS LEU ILE HIS ALA ALA
SEQRES 32 A 450 ILE ASP THR TYR ASP ASP HIS ARG MET ALA MET CYS PHE
SEQRES 33 A 450 SER LEU VAL ALA LEU SER ASP THR PRO VAL THR ILE ASN
SEQRES 34 A 450 ASP PRO LYS CYS THR SER LYS THR PHE PRO ASP TYR PHE
SEQRES 35 A 450 ASP LYS PHE ALA GLN LEU SER ARG
HET S3P A 427 16
HET SKM A 428 12
HET GPJ A 429 10
HET MG A 430 1
HET MG A 431 1
HET MG A 432 1
HET CL A 433 1
HET CL A 434 1
HET CL A 435 1
HET CL A 436 1
HET EPE A 437 21
HET PO4 A 438 5
HETNAM S3P SHIKIMATE-3-PHOSPHATE
HETNAM SKM (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC
HETNAM 2 SKM ACID
HETNAM GPJ GLYPHOSATE
HETNAM MG MAGNESIUM ION
HETNAM CL CHLORIDE ION
HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HETNAM PO4 PHOSPHATE ION
HETSYN SKM SHIKIMATE
HETSYN EPE HEPES
FORMUL 2 S3P C7 H11 O8 P
FORMUL 3 SKM C7 H10 O5
FORMUL 4 GPJ C3 H9 N O5 P 1+
FORMUL 5 MG 3(MG 2+)
FORMUL 8 CL 4(CL 1-)
FORMUL 12 EPE C8 H18 N2 O4 S
FORMUL 13 PO4 O4 P 3-
FORMUL 14 HOH *747(H2 O)
HELIX 1 1 SER A 21 ALA A 35 1 15
HELIX 2 2 SER A 47 LEU A 60 1 14
HELIX 3 3 ALA A 95 LEU A 106 1 12
HELIX 4 4 GLU A 118 ARG A 124 5 7
HELIX 5 5 ILE A 126 ALA A 136 1 11
HELIX 6 6 SER A 171 ALA A 181 1 11
HELIX 7 7 PRO A 182 ALA A 184 5 3
HELIX 8 8 SER A 198 PHE A 212 1 15
HELIX 9 9 ASP A 243 GLY A 258 1 16
HELIX 10 10 GLN A 272 ILE A 275 5 4
HELIX 11 11 GLN A 276 GLY A 285 1 10
HELIX 12 12 ALA A 315 ALA A 323 1 9
HELIX 13 13 LEU A 324 ALA A 326 5 3
HELIX 14 14 VAL A 335 LYS A 341 5 7
HELIX 15 15 ASP A 344 VAL A 356 1 13
HELIX 16 16 ASP A 385 LEU A 394 1 10
HELIX 17 17 VAL A 395 SER A 398 5 4
HELIX 18 18 PRO A 407 THR A 413 5 7
HELIX 19 19 ASP A 416 LEU A 424 1 9
SHEET 1 A 3 SER A 3 LEU A 6 0
SHEET 2 A 3 VAL A 402 ASN A 405 -1 O ILE A 404 N LEU A 4
SHEET 3 A 3 ALA A 379 ILE A 380 1 N ILE A 380 O THR A 403
SHEET 1 B 2 LEU A 11 ILE A 12 0
SHEET 2 B 2 SER A 425 ARG A 426 -1 O ARG A 426 N LEU A 11
SHEET 1 C 4 GLY A 14 ASN A 17 0
SHEET 2 C 4 GLU A 260 THR A 264 1 O THR A 264 N VAL A 16
SHEET 3 C 4 TYR A 294 ARG A 298 -1 O VAL A 295 N VAL A 263
SHEET 4 C 4 GLN A 287 TRP A 290 -1 N GLU A 289 O ILE A 296
SHEET 1 D 4 ASN A 63 LEU A 66 0
SHEET 2 D 4 CYS A 73 GLU A 76 -1 O GLU A 76 N ASN A 63
SHEET 3 D 4 THR A 38 THR A 42 -1 N LEU A 41 O CYS A 73
SHEET 4 D 4 GLN A 237 LEU A 239 1 O PHE A 238 N ARG A 40
SHEET 1 E 4 LEU A 88 PHE A 91 0
SHEET 2 E 4 ASP A 112 THR A 116 1 O VAL A 114 N LEU A 90
SHEET 3 E 4 LEU A 151 GLN A 154 -1 O ILE A 153 N TYR A 113
SHEET 4 E 4 GLN A 139 TYR A 142 -1 N GLU A 141 O ARG A 152
SHEET 1 F 4 GLY A 161 ILE A 165 0
SHEET 2 F 4 VAL A 188 ILE A 192 1 O LYS A 191 N VAL A 163
SHEET 3 F 4 GLU A 223 ILE A 226 -1 O PHE A 224 N ILE A 190
SHEET 4 F 4 ILE A 217 HIS A 219 -1 N ILE A 217 O VAL A 225
SHEET 1 G 4 ASP A 306 ASP A 308 0
SHEET 2 G 4 THR A 330 ARG A 333 1 O ARG A 333 N LEU A 307
SHEET 3 G 4 PHE A 366 THR A 370 -1 O ILE A 369 N THR A 330
SHEET 4 G 4 THR A 359 GLU A 362 -1 N THR A 359 O THR A 370
LINK OE1AGLU A 123 MG A MG A 430 1555 1555 2.02
LINK OE1AGLN A 145 MG A MG A 430 1555 1555 2.08
LINK MG A MG A 430 O HOH A 871 1555 1555 2.04
LINK MG A MG A 430 O HOH A 901 1555 1555 2.08
LINK MG A MG A 430 O AHOH A 927 1555 1555 2.04
LINK MG A MG A 430 O AHOH A1041 1555 1555 2.12
LINK MG A MG A 431 O AHOH A 608 1555 1555 2.13
LINK MG A MG A 431 O HOH A 732 1555 1555 1.98
LINK MG A MG A 431 O HOH A 733 1555 1555 2.00
LINK MG A MG A 431 O AHOH A 734 1555 1555 2.00
LINK MG A MG A 431 O HOH A 735 1555 1555 2.16
LINK MG A MG A 431 O HOH A1102 1555 1555 2.11
LINK MG A MG A 432 O AHOH A 533 1555 1555 2.07
LINK MG A MG A 432 O HOH A 740 1555 1555 2.16
LINK MG A MG A 432 O AHOH A 741 1555 1555 1.97
LINK MG A MG A 432 O AHOH A 742 1555 1555 1.90
LINK MG A MG A 432 O HOH A 743 1555 1555 2.17
LINK MG A MG A 432 O AHOH A 744 1555 1555 2.06
CISPEP 1 PRO A 149 PRO A 150 0 1.93
CISPEP 2 GLY A 258 GLY A 259 0 -2.61
SITE 1 AC1 16 LYS A 22 SER A 23 ARG A 27 THR A 97
SITE 2 AC1 16 SER A 170 SER A 171 GLN A 172 SER A 198
SITE 3 AC1 16 TYR A 201 ASP A 314 ASN A 337 LYS A 341
SITE 4 AC1 16 GPJ A 429 HOH A 503 HOH A 725 HOH A 826
SITE 1 AC2 11 LYS A 22 SER A 23 ARG A 27 THR A 97
SITE 2 AC2 11 GLN A 172 TYR A 201 ASP A 314 LYS A 341
SITE 3 AC2 11 GPJ A 429 PO4 A 438 HOH A 503
SITE 1 AC3 15 LYS A 22 ASN A 94 GLY A 96 ARG A 124
SITE 2 AC3 15 GLN A 172 ASP A 314 GLU A 342 ARG A 345
SITE 3 AC3 15 HIS A 386 ARG A 387 LYS A 412 S3P A 427
SITE 4 AC3 15 SKM A 428 HOH A 604 HOH A 826
SITE 1 AC4 7 GLU A 123 GLN A 145 HOH A 753 HOH A 871
SITE 2 AC4 7 HOH A 901 HOH A 927 HOH A1041
SITE 1 AC5 6 HOH A 608 HOH A 732 HOH A 733 HOH A 734
SITE 2 AC5 6 HOH A 735 HOH A1102
SITE 1 AC6 8 HOH A 524 HOH A 533 HOH A 740 HOH A 741
SITE 2 AC6 8 HOH A 742 HOH A 743 HOH A 744 HOH A 953
SITE 1 AC7 3 ASP A 293 ARG A 354 VAL A 360
SITE 1 AC8 3 ASN A 17 LYS A 420 GLN A 423
SITE 1 AC9 4 ALA A 378 ALA A 379 HOH A 579 HOH A 971
SITE 1 BC1 4 ARG A 354 GLU A 362 HOH A 745 HOH A 866
SITE 1 BC2 6 LYS A 268 ASP A 279 TRP A 290 HOH A 738
SITE 2 BC2 6 HOH A 751 HOH A 861
SITE 1 BC3 9 SER A 170 SER A 171 VAL A 197 SER A 198
SITE 2 BC3 9 ASN A 337 LYS A 341 SKM A 428 HOH A 725
SITE 3 BC3 9 HOH A 826
CRYST1 43.866 87.484 49.994 90.00 105.26 90.00 P 1 21 1 2
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 0.022797 0.000000 0.006219 0.00000
SCALE2 0.000000 0.011431 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020733 0.00000