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- PDB-7xuy: Crystal structure of 5-chloro-2-hydroxymuconate tautomerase CnbG -

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Basic information

Entry
Database: PDB / ID: 7xuy
TitleCrystal structure of 5-chloro-2-hydroxymuconate tautomerase CnbG
ComponentsTautomerase
KeywordsISOMERASE / catechol meta-cleavage pathway / beta-alpha-beta block / chloronitrobenzene degradation / hexamer
Function / homologyIsomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / 4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Tautomerase/MIF superfamily / isomerase activity / Tautomerase
Function and homology information
Biological speciesComamonas testosteroni CNB-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsMa, H.L. / Li, D.F.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFC1808801 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural insights into the substrate specificity of 5-chloro-2-hydroxymuconate tautomerase CnbG.
Authors: Ma, H.L. / Ding, M. / Guo, L. / Li, D.F.
History
DepositionMay 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tautomerase


Theoretical massNumber of molelcules
Total (without water)8,1111
Polymers8,1111
Non-polymers00
Water1448
1
A: Tautomerase
x 6


Theoretical massNumber of molelcules
Total (without water)48,6686
Polymers48,6686
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area12630 Å2
ΔGint-70 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.407, 81.407, 63.678
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Tautomerase


Mass: 8111.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni CNB-1 (bacteria)
Gene: cnbG / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q38M36, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 310.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2M (NH4)2SO4, 0.1 M Tris

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.26 Å / Num. obs: 5614 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 40.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.055 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 409 / CC1/2: 0.857 / Rrim(I) all: 0.58

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
PHENIX1.14_3260phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FAZ

4faz


Resolution: 2.001→30.84 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / Phase error: 18.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 292 5 %Random
Rwork0.1778 5317 --
obs-5609 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.69 Å2 / Biso mean: 59.7908 Å2 / Biso min: 34 Å2
Refinement stepCycle: final / Resolution: 2.001→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 0 8 520
Biso mean---57.86 -
Num. residues----64
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.001-2.52020.23631390.21532632
2.5202-30.830.19481530.17052685
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)
16.4015-2.11330.39277.6615-2.26627.6639-0.08320.44340.5358-1.1197-0.1105-0.63140.31120.3040.39120.4328-0.01280.04450.401-0.02210.41179.26921.701424.7036
23.5561-0.14840.88996.02210.04442.9452-0.1426-0.14-0.3021-0.1822-0.2477-1.53270.87711.19280.11550.44760.19460.02250.7883-0.12850.698218.2726-5.89429.6846
33.7874-0.9783-1.38187.9812-0.46394.2680.00120.32570.1051-0.37720.03630.0463-0.46950.3704-0.02720.481-0.0220.00290.43230.02470.35774.59776.604823.2133
42.67472.9758-0.73965.09290.73096.925-0.3831.59430.8079-0.8885-0.48350.2980.03021.46020.14291.119-0.1280.04380.66680.27950.87376.808620.705916.102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 38 )A13 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 56 )A39 - 56
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 64 )A57 - 64

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