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- PDB-8khg: Itaconyl-CoA hydratase PaIch -

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Basic information

Entry
Database: PDB / ID: 8khg
TitleItaconyl-CoA hydratase PaIch
ComponentsItaconyl-CoA hydratase
KeywordsUNKNOWN FUNCTION / itaconyl-CoA hydratase
Function / homology: / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / HotDog domain superfamily / CITRIC ACID / Itaconyl-CoA hydratase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuang, Q. / Bao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural and functional characterization of itaconyl-CoA hydratase and citramalyl-CoA lyase involved in itaconate metabolism of Pseudomonas aeruginosa.
Authors: Huang, Q. / Duan, C. / Ma, H. / Nong, C. / Zheng, Q. / Zhou, J. / Zhao, N. / Mou, X. / Liu, T. / Zou, S. / Yang, N. / Tong, A. / Qin, W. / Bao, R.
History
DepositionAug 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Itaconyl-CoA hydratase
B: Itaconyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5094
Polymers61,1252
Non-polymers3842
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-16 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.326, 103.653, 109.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Itaconyl-CoA hydratase


Mass: 30562.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CAZ10_11905 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q7L2
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Ammonium citratetribasic, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→39.44 Å / Num. obs: 16622 / % possible obs: 99.3 % / Redundancy: 12.8 % / Biso Wilson estimate: 27.88 Å2 / CC1/2: 0.997 / Net I/σ(I): 20.9
Reflection shellResolution: 2.6→2.9 Å / Num. unique obs: 1196 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.44 Å / SU ML: 0.3319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2619 1651 9.93 %
Rwork0.195 14971 -
obs0.2017 16622 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.77 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 26 14 4305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834423
X-RAY DIFFRACTIONf_angle_d1.00166027
X-RAY DIFFRACTIONf_chiral_restr0.0489607
X-RAY DIFFRACTIONf_plane_restr0.0095817
X-RAY DIFFRACTIONf_dihedral_angle_d16.89871617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.311360.24971196X-RAY DIFFRACTION98.45
2.68-2.760.30341260.23091238X-RAY DIFFRACTION98.55
2.76-2.860.32621450.23051195X-RAY DIFFRACTION98.46
2.86-2.980.32531320.22851232X-RAY DIFFRACTION98.77
2.98-3.110.29711380.21751242X-RAY DIFFRACTION98.92
3.11-3.280.26751330.20431238X-RAY DIFFRACTION98.85
3.28-3.480.30761340.20171214X-RAY DIFFRACTION98.61
3.48-3.750.2611420.18711246X-RAY DIFFRACTION98.79
3.75-4.130.24981370.17461261X-RAY DIFFRACTION99.29
4.13-4.720.20421430.15541262X-RAY DIFFRACTION99.43
4.72-5.950.2171410.18441288X-RAY DIFFRACTION99.51
5.95-39.440.23361440.18971359X-RAY DIFFRACTION98.43

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