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- PDB-5xwb: Crystal Structure of 5-Enolpyruvulshikimate-3-phosphate Synthase ... -

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Basic information

Entry
Database: PDB / ID: 5xwb
TitleCrystal Structure of 5-Enolpyruvulshikimate-3-phosphate Synthase from a Psychrophilic Bacterium, Colwellia psychrerythraea
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / shikimate pathway glyphosate psychrophiles Colwellia psychrerythraea cold-adapted enzyme
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 speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, J.H. / Kim, H.J. / Choi, J.M. / Kim, D.-W. / Seo, Y.-S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of 5-enolpyruvylshikimate-3-phosphate synthase from a psychrophilic bacterium, Colwellia psychrerythraea 34H.
Authors: Lee, J.H. / Choi, J.M. / Kim, H.J.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-phosphoshikimate 1-carboxyvinyltransferase
B: 3-phosphoshikimate 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)96,9062
Polymers96,9062
Non-polymers00
Water7,080393
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)48,4531
Polymers48,4531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)48,4531
Polymers48,4531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.798, 80.027, 82.271
Angle α, β, γ (deg.)90.00, 96.46, 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 / EPSPS


Mass: 48453.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria)
Strain: 34H / ATCC BAA-681 / Gene: aroA, CPS_2333 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q482G5, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: sharp rod-like shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, soidum chloride, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40348 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 25.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NVS

3nvs


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.881 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.199 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 2024 5 %RANDOM
Rwork0.14627 ---
obs0.14947 38306 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.612 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 0 393 6875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196590
X-RAY DIFFRACTIONr_bond_other_d0.0020.026264
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9748936
X-RAY DIFFRACTIONr_angle_other_deg1.021314576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91525.538260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.352151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9461522
X-RAY DIFFRACTIONr_chiral_restr0.1090.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217276
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021194
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4962.8533406
X-RAY DIFFRACTIONr_mcbond_other2.4912.8523405
X-RAY DIFFRACTIONr_mcangle_it3.6654.2684254
X-RAY DIFFRACTIONr_mcangle_other3.6654.2694255
X-RAY DIFFRACTIONr_scbond_it4.143.4453184
X-RAY DIFFRACTIONr_scbond_other4.1393.4453184
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4414.934683
X-RAY DIFFRACTIONr_long_range_B_refined7.83235.3737256
X-RAY DIFFRACTIONr_long_range_B_other7.82235.2057201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 160 -
Rwork0.139 2734 -
obs--97.51 %

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