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- PDB-4lj2: Crystal structure of chorismate synthase from Acinetobacter bauma... -

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Basic information

Entry
Database: PDB / ID: 4lj2
TitleCrystal structure of chorismate synthase from Acinetobacter baumannii at 3.15A resolution
ComponentsChorismate synthase
KeywordsLYASE
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: 3.15 Å
AuthorsChaudhary, A. / Singh, N. / Kaushik, S. / Tyagi, T.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of chorismate synthase from Acinetobacter baumannii at 3.15A resolution
Authors: Chaudhary, A. / Singh, N. / Kaushik, S. / Tyagi, T.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: 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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-29 kcal/mol
Surface area33810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.770, 72.610, 89.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C7F3, chorismate synthase

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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: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Tris-HCl, 0.2M MgCl2, 20% PEG3350, pH 8, 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: May 1, 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: 3.15→46.54 Å / Num. all: 12779 / Num. obs: 12153 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.7 Å2
Reflection shellResolution: 3.15→3.24 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R52

1r52


Resolution: 3.15→46.54 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1394503.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 654 5.1 %RANDOM
Rwork0.225 ---
all0.24 12779 --
obs0.225 12153 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.1423 Å2 / ksol: 0.329481 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.81 Å20 Å20 Å2
2---1.82 Å20 Å2
3---10.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 3.15→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 0 0 4840
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d2.67
X-RAY DIFFRACTIONc_mcbond_it2.931.5
X-RAY DIFFRACTIONc_mcangle_it4.952
X-RAY DIFFRACTIONc_scbond_it3.562
X-RAY DIFFRACTIONc_scangle_it4.952.5
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 100 4.9 %
Rwork0.253 1941 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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