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- PDB-5z9a: Crystal structure of chorismate synthase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5z9a
TitleCrystal structure of chorismate synthase from Pseudomonas aeruginosa
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
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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsIqbal, N. / Chaudhary, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of chorismate synthase from Pseudomonas aeruginosa
Authors: Iqbal, N. / Chaudhary, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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 / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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

Downloads & links

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Assembly

Deposited unit
A: Chorismate synthase
B: Chorismate synthase


Theoretical massNumber of molelcules
Total (without water)78,0722
Polymers78,0722
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-22.4 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.530, 76.530, 389.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 1 - 349 / Label seq-ID: 1 - 349

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.769773, 0.403496, -0.494611), (0.38891, -0.31797, -0.864664), (-0.50616, -0.857954, 0.087841)-4.80829, 40.1577, 29.65774

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Components

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


Mass: 39036.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain LESB58) (bacteria)
Strain: LESB58 / Gene: aroC, PLES_36461 / Production host: Escherichia coli (E. coli) / References: UniProt: B7UV40, chorismate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 10mM HEPES pH 7.5, 8% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.79→66.28 Å / Num. obs: 17307 / % possible obs: 96.36 % / Redundancy: 5.92 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.05
Reflection shellResolution: 2.791→2.891 Å / Rmerge(I) obs: 0.43 / Num. measured obs: 7302 / Num. unique obs: 887

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R53

1r53


Resolution: 2.79→66.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 34.162 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.898 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27602 864 5 %RANDOM
Rwork0.20701 ---
obs0.21027 16443 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.169 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å2-0 Å2
2---0.8 Å2-0 Å2
3---2.59 Å2
Refinement stepCycle: 1 / Resolution: 2.79→66.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 0 20 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193736
X-RAY DIFFRACTIONr_bond_other_d0.010.023698
X-RAY DIFFRACTIONr_angle_refined_deg2.6041.9885048
X-RAY DIFFRACTIONr_angle_other_deg3.70438498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00224.054148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.10215628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4331529
X-RAY DIFFRACTIONr_chiral_restr0.1430.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214226
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02779
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_it4.4627.5441976
X-RAY DIFFRACTIONr_mcbond_other4.4637.5411975
X-RAY DIFFRACTIONr_mcangle_it6.99311.2882453
X-RAY DIFFRACTIONr_mcangle_other6.99211.2922454
X-RAY DIFFRACTIONr_scbond_it5.428.4141760
X-RAY DIFFRACTIONr_scbond_other5.4198.4181761
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.54412.3142596
X-RAY DIFFRACTIONr_long_range_B_refined14.14772.71115085
X-RAY DIFFRACTIONr_long_range_B_other14.14772.71315084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2190 / Type: tight thermal / Rms dev position: 6.31 Å / Weight position: 0.5
LS refinement shellResolution: 2.791→2.863 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 66 -
Rwork0.305 1216 -
obs--99.92 %
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)
10.7090.3791-0.69761.7938-0.72120.8225-0.02310.14750.01250.04540.08090.2234-0.1618-0.1989-0.05780.44140.1315-0.03860.08060.00920.0718-11.846327.902323.3116
20.1408-0.0105-0.35410.6252-0.34761.2162-0.02960.0061-0.0269-0.173-0.0677-0.04630.05780.01050.09730.213-0.00670.00920.07550.03710.0554.03126.46713.6611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 349
2X-RAY DIFFRACTION2B1 - 349

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