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- PDB-4ob9: Crystal structure of chorismate synthase from Acinetobacter bauma... -

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Basic information

Entry
Database: PDB / ID: 4ob9
TitleCrystal structure of chorismate synthase from Acinetobacter baumannii at 2.50A resolution
ComponentsChorismate synthase
KeywordsLYASE / Chorismate synthase / synthase
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / FMN binding / cytosol
Similarity search - Function
Chorismate synthase signature 3. / Chorismate synthase, AroC fold / Chorismate synthase AroC / Chorismate synthase signature 2. / Chorismate synthase / Chorismate synthase, conserved site / Chorismate synthase AroC superfamily / Chorismate synthase / Chorismate synthase signature 1. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShukla, P.K. / Chaudhary, A. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of chorismate synthase from Acinetobacter baumannii at 2.50A resolution
Authors: Shukla, P.K. / Chaudhary, A. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJan 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chorismate synthase
B: Chorismate synthase


Theoretical massNumber of molelcules
Total (without water)78,1022
Polymers78,1022
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-29 kcal/mol
Surface area30600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.980, 89.790, 108.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Chorismate synthase / 5-enolpyruvylshikimate-3-phosphate phospholyase


Mass: 39051.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 19606 / Gene: aroC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: D0C7F3, chorismate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Tris-HCl, 0.2M MgCl2, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 13, 2013 / Details: mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→108.38 Å / Num. all: 23133 / Num. obs: 23133 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.18 / Net I/σ(I): 5.9
Reflection shellResolution: 2.5→2.55 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.69 / % possible all: 94

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJ2

4lj2


Resolution: 2.5→50.19 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.878 / SU B: 9.695 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.83 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26425 1166 5 %RANDOM
Rwork0.21793 ---
all0.22036 23133 --
obs0.22036 21930 91.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å20 Å2
2--2.56 Å2-0 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 0 211 4881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194752
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9646426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09723.9200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.72615788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4721536
X-RAY DIFFRACTIONr_chiral_restr0.1220.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213606
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 79 -
Rwork0.314 1532 -
obs--93.39 %

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