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- PDB-7crd: Structure of Pseudomonas aeruginosa OdaA -

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Basic information

Entry
Database: PDB / ID: 7crd
TitleStructure of Pseudomonas aeruginosa OdaA
ComponentsProbable enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Pseudomonas aeruginosa / crotonase
Function / homology: / delta(3)-delta(2)-enoyl-CoA isomerase activity / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / Probable enoyl-CoA hydratase/isomerase
Function and homology information
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
DepositionAug 13, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 16, 2020ID: 7BOQ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 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
D: Probable enoyl-CoA hydratase/isomerase
A: Probable enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)56,3752
Polymers56,3752
Non-polymers00
Water2,432135
1
D: Probable enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)28,1881
Polymers28,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)28,1881
Polymers28,1881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.391, 81.391, 60.423
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-310-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG6000, 0.1 M sodium citrate tribasic dehydrate pH 5.0

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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 S 6M / Detector: PIXEL / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→28 Å / Num. obs: 35138 / % possible obs: 99.48 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.62 Å2 / Rrim(I) all: 0.105 / Rsym value: 0.099 / Net I/σ(I): 23.61
Reflection shellResolution: 1.901→1.969 Å / Num. unique obs: 3505 / Rrim(I) all: 0.54 / Rsym value: 0.509 / % possible all: 98.43

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nek

4nek


Resolution: 1.901→26.64 Å / SU ML: 0.1356 / Cross valid method: FREE R-VALUE / Phase error: 18.559 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1875 2023 -
Rwork0.1714 33078 -
obs-35100 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.41 Å2
Refinement stepCycle: LAST / Resolution: 1.901→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 0 135 3913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113840
X-RAY DIFFRACTIONf_angle_d1.26235192
X-RAY DIFFRACTIONf_chiral_restr0.3091604
X-RAY DIFFRACTIONf_plane_restr0.0075680
X-RAY DIFFRACTIONf_dihedral_angle_d26.61351440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.950.22081420.18452386X-RAY DIFFRACTION97.98
1.95-20.2031500.18392294X-RAY DIFFRACTION99.76
2-2.060.22561290.18742401X-RAY DIFFRACTION99.88
2.06-2.130.22761390.18162366X-RAY DIFFRACTION99.48
2.13-2.20.21081500.18032389X-RAY DIFFRACTION99.53
2.2-2.290.20551400.18192370X-RAY DIFFRACTION100
2.29-2.390.18141470.1812370X-RAY DIFFRACTION100
2.39-2.520.19971440.17992366X-RAY DIFFRACTION99.68
2.52-2.680.20631500.1842339X-RAY DIFFRACTION99.92
2.68-2.890.18371460.17732385X-RAY DIFFRACTION99.61
2.89-3.180.18411420.17962367X-RAY DIFFRACTION100
3.18-3.630.16661500.162368X-RAY DIFFRACTION99.8
3.63-4.580.14481450.142351X-RAY DIFFRACTION99.28
4.58-90.16691490.16142326X-RAY DIFFRACTION98.33
Refinement TLS params.Method: refined / Origin x: -33.9295079491 Å / Origin y: 46.0903891283 Å / Origin z: -94.3761312686 Å
111213212223313233
T0.163578568585 Å20.0091126528138 Å2-0.0373634674816 Å2-0.167428891899 Å2-0.00117513275549 Å2--0.177745917679 Å2
L0.588697715957 °20.199791512822 °2-0.481151164424 °2-0.0537666160062 °2-0.189325282995 °2--0.486280816042 °2
S-0.0146098838428 Å °0.0440316253528 Å °0.0670767613424 Å °-0.00268373324865 Å °0.0471367622576 Å °0.0397219416422 Å °-0.0432155385101 Å °-0.0550510284109 Å °-0.0415213287282 Å °
Refinement TLS groupSelection details: all

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