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- PDB-3ti2: 1.90 Angstrom resolution crystal structure of N-terminal domain 3... -

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Basic information

Entry
Database: PDB / ID: 3ti2
Title1.90 Angstrom resolution crystal structure of N-terminal domain 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / EPSP SYNTHASE
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) ...EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLight, S.H. / Minasov, G. / Halavaty, A.S. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.90 Angstrom resolution crystal structure of N-terminal domain 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae
Authors: Light, S.H. / Minasov, G. / Halavaty, A.S. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-phosphoshikimate 1-carboxyvinyltransferase
B: 3-phosphoshikimate 1-carboxyvinyltransferase
C: 3-phosphoshikimate 1-carboxyvinyltransferase
D: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,94717
Polymers98,1684
Non-polymers77813
Water12,178676
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6484
Polymers24,5421
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0015
Polymers24,5421
Non-polymers4594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6484
Polymers24,5421
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6484
Polymers24,5421
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.758, 40.072, 133.861
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS


Mass: 24542.020 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: aroA, VC_1732 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9KRB0, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT CRYSTALLIZATION WAS SETUP WITH N-TERMINAL EXPRESSION TAG ...AUTHOR STATES THAT CRYSTALLIZATION WAS SETUP WITH N-TERMINAL EXPRESSION TAG (MHHHHHHSSGVDLGTENLYFQSNA) PLUS THE FULL LENGTH PROTEIN (UNP Q9KRB0 RESIDUES 1-243) BUT ONLY OBSERVED THE N-TERMINAL DOMAIN IN THE CRYSTAL STRUCTURE. BASED ON AN ANALYSIS OF THE CRYSTAL LATTICE, IT IS CLEAR THAT IT ISN'T A MATTER OF THE C-TERMINAL DOMAIN BEING DISORDERED BUT RATHER THE DOMAIN IS NOT PRESENT IN THE CRYSTAL, PRESUMABLY CONTAMINANT PROTEASE CLEAVED IT OFF. AUTHOR ALSO THINKS THAT EXPRESSION TAG AND THE FIRST 15 N-TERMINAL RESIDUES HAVE BEEN CLEAVED OFF. SEQRES RECORD PRESENTED HERE CONTAINS UNP Q9KRB0 RESIDUES 16-243.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 4.0 mGr/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCl (pH 8.3) Crystallization: Classics II (Qiagen) condition D10 0.1 M Bis-Tris pH 6.5 20% (w/v) PEG 5000 MME, VAPOR DIFFUSION, ...Details: Protein: 4.0 mGr/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCl (pH 8.3) Crystallization: Classics II (Qiagen) condition D10 0.1 M Bis-Tris pH 6.5 20% (w/v) PEG 5000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2011 / Details: BERYLLIUM LENS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 65572 / Num. obs: 65572 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3198 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NVS

3nvs


Resolution: 1.9→29.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.994 / SU ML: 0.089
Isotropic thermal model: thermal factors individually refined
Cross valid method: THROUGHOUT / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19557 3330 5.1 %RANDOM
Rwork0.15107 ---
all0.1534 62231 --
obs0.1534 62231 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.036 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.54 Å2
2---0.52 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6847 0 37 676 7560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.027188
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9849793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9945962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27925.016305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.516151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0491538
X-RAY DIFFRACTIONr_chiral_restr0.1480.21152
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215410
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 228 -
Rwork0.225 4118 -
obs-4118 95.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72230.2803-0.1731.38920.17140.725-0.0162-0.0006-0.03050.0498-0.0060.03530.0226-0.02070.02230.0272-0.00590.00050.0053-0.00350.02818.01250.312419.2272
20.58280.1199-0.21740.3476-0.33761.0348-0.04060.0544-0.011-0.071-0.0012-0.03760.0391-0.01070.04180.0290.00430.00820.0096-0.00650.038325.85951.16215.0782
30.83160.120.0780.93980.20740.79860.0361-0.0602-0.02470.063-0.00750.0210.0410.0058-0.02870.02870.0012-0.01020.01640.01210.023964.78179.072465.9258
40.6779-0.19340.39310.1436-0.16721.10170.01550.040.0061-0.0478-0.00170.03670.0454-0.0316-0.01390.03590.003-0.01510.0146-0.00550.047558.80739.543950.7422
51.00840.1578-0.37430.9840.09551.3783-0.05390.0856-0.0228-0.0446-0.0021-0.10110.0559-0.05460.0560.0274-0.0050.01550.0249-0.0110.022337.007618.75440.1005
61.3195-0.3827-1.04830.42050.31511.91930.00250.2289-0.0560.0283-0.11140.05480.0175-0.34970.10890.0094-0.01370.00360.1111-0.04130.020722.131819.82646.4791
70.97320.06590.18411.2789-0.26560.6141-0.01530.00350.0230.001-0.0051-0.08260.02830.02120.02040.02210.01980.0110.02180.00410.027219.916810.5794-18.5174
81.7143-0.2751-0.07310.2902-0.00570.30530.04070.08640.048-0.074-0.01970.07220.0071-0.0773-0.02110.04240.0168-0.01110.03330.00780.03455.071411.0608-25.4488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 119
2X-RAY DIFFRACTION2A120 - 243
3X-RAY DIFFRACTION3B18 - 119
4X-RAY DIFFRACTION4B120 - 242
5X-RAY DIFFRACTION5C16 - 119
6X-RAY DIFFRACTION6C120 - 243
7X-RAY DIFFRACTION7D17 - 119
8X-RAY DIFFRACTION8D120 - 242

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