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- PDB-5wuy: Crystal structure of chorismate synthase from Acinetobacter bauma... -

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Basic information

Entry
Database: PDB / ID: 5wuy
TitleCrystal structure of chorismate synthase from Acinetobacter baumannii at 2.50A 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
Chorismate synthase / Chorismate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIqbal, N. / Chaudhary, A. / Shukla, K.P. / 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: Iqbal, N. / Chaudhary, A. / Shukla, K.P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-29 kcal/mol
Surface area24690 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 352

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Chorismate synthase / CS / 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) / Gene: aroC / Production host: Escherichia coli (E. coli)
References: UniProt: A0A081GZ37, UniProt: B0VDX7*PLUS, chorismate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 13, 2013 / Details: MIRROR
RadiationProtocol: 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. obs: 23133 / % possible obs: 92 % / Redundancy: 4.6 % / Rsym value: 0.18 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.55 Å / Mean I/σ(I) obs: 1.8 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OB9

4ob9


Resolution: 2.5→89.79 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.764 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.549 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25295 1166 5 %RANDOM
Rwork0.2127 ---
obs0.21481 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: 47.942 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--2.59 Å2-0 Å2
3----3.19 Å2
Refinement stepCycle: 1 / Resolution: 2.5→89.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 0 205 4357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194214
X-RAY DIFFRACTIONr_bond_other_d0.0090.024152
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9625685
X-RAY DIFFRACTIONr_angle_other_deg1.6739526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72623.977176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.55715708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0141532
X-RAY DIFFRACTIONr_chiral_restr0.1080.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214792
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02920
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_it3.594.5362222
X-RAY DIFFRACTIONr_mcbond_other3.5734.5352221
X-RAY DIFFRACTIONr_mcangle_it5.9776.7462760
X-RAY DIFFRACTIONr_mcangle_other5.986.7482761
X-RAY DIFFRACTIONr_scbond_it3.5475.0941992
X-RAY DIFFRACTIONr_scbond_other3.5475.0961993
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9127.4352926
X-RAY DIFFRACTIONr_long_range_B_refined11.80941.8918307
X-RAY DIFFRACTIONr_long_range_B_other11.80941.87918273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 30962 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 84 -
Rwork0.304 1651 -
obs--93.83 %

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