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- PDB-7bor: Structure of Pseudomonas aeruginosa CoA-bound OdaA -

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Basic information

Entry
Database: PDB / ID: 7bor
TitleStructure of Pseudomonas aeruginosa CoA-bound OdaA
ComponentsProbable enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Pseudomonas aeruginosa / crotonase
Function / homology
Function and homology information


delta(3)-delta(2)-enoyl-CoA isomerase activity / peroxisome
Similarity search - Function
: / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Probable enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsZhao, N. / Zhao, C. / Liu, L. / Li, T. / Li, C. / He, L. / Zhu, Y. / Song, Y. / Bao, R.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Structural and molecular dynamic studies of Pseudomonas aeruginosa OdaA reveal the regulation role of a C-terminal hinge element.
Authors: Zhao, N.L. / Zhang, Q.Q. / Zhao, C. / Liu, L. / Li, T. / Li, C.C. / He, L.H. / Zhu, Y.B. / Song, Y.J. / Liu, H.X. / Bao, R.
History
DepositionMar 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0Aug 26, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / reflns / software
Item: _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_special_symmetry.auth_seq_id ..._pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_high / _reflns.d_resolution_low
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Nov 29, 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: Probable enoyl-CoA hydratase/isomerase
C: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9104
Polymers56,3752
Non-polymers1,5352
Water3,261181
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A: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9552
Polymers28,1881
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint0 kcal/mol
Surface area11280 Å2
MethodPISA
2
C: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9552
Polymers28,1881
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint1 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.546, 81.546, 59.174
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
Components on special symmetry positions
IDModelComponents
11A-438-

HOH

21A-482-

HOH

31C-401-

HOH

41C-421-

HOH

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Components

#1: Protein Probable enoyl-CoA hydratase/isomerase


Mass: 28187.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4330 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HW71
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 20% Tacsimate, 2% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→30.32 Å / Num. obs: 34519 / % possible obs: 99.62 % / Redundancy: 4.6 % / Biso Wilson estimate: 32.94 Å2 / CC1/2: 0.958 / CC star: 0.989 / Rrim(I) all: 0.073 / Rsym value: 0.065 / Net I/σ(I): 17.96
Reflection shellResolution: 1.901→1.969 Å / Mean I/σ(I) obs: 1.47 / Num. unique obs: 3452 / CC1/2: 0.915 / CC star: 0.987 / Rrim(I) all: 0.677 / Rsym value: 0.587

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nek

4nek


Resolution: 1.901→26.69 Å / SU ML: 0.2775 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.0387 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2259 2000 5.8 %
Rwork0.1893 32498 -
obs0.1914 34498 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.65 Å2
Refinement stepCycle: LAST / Resolution: 1.901→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 96 181 4055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01473940
X-RAY DIFFRACTIONf_angle_d1.42895342
X-RAY DIFFRACTIONf_chiral_restr0.0636614
X-RAY DIFFRACTIONf_plane_restr0.0099686
X-RAY DIFFRACTIONf_dihedral_angle_d25.63591492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.950.35951440.30882299X-RAY DIFFRACTION99.43
1.95-20.31761400.28652318X-RAY DIFFRACTION99.51
2-2.060.30211450.26092317X-RAY DIFFRACTION99.56
2.06-2.130.29361380.2332334X-RAY DIFFRACTION99.76
2.13-2.20.29391480.23532325X-RAY DIFFRACTION99.76
2.2-2.290.30711470.22782327X-RAY DIFFRACTION99.76
2.29-2.40.25941420.21842348X-RAY DIFFRACTION99.68
2.4-2.520.27231440.21982302X-RAY DIFFRACTION99.71
2.52-2.680.24461380.20932312X-RAY DIFFRACTION100
2.68-2.890.27361430.20482350X-RAY DIFFRACTION99.84
2.89-3.180.25481390.20632301X-RAY DIFFRACTION99.92
3.18-3.640.20111390.17992339X-RAY DIFFRACTION99.84
3.64-4.580.17641520.14212340X-RAY DIFFRACTION99.8
4.58-100.16941410.15372286X-RAY DIFFRACTION98.46

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