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- PDB-4fdx: Kinetic and structural characterization of the 4-oxalocrotonate t... -

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Basic information

Entry
Database: PDB / ID: 4fdx
TitleKinetic and structural characterization of the 4-oxalocrotonate tautomerase isozymes from Methylibium petroleiphilum
Components4-oxalocrotonase tautomerase isozyme
KeywordsISOMERASE / alpha/beta barrel / 4OT / Tautomerase superfamily
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethylibium petroleiphilum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsTerrell, C.R. / Hoffman, D.W. / Whitman, C.P.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Structural and kinetic characterization of two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1.
Authors: Terrell, C.R. / Burks, E.A. / Whitman, C.P. / Hoffman, D.W.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-oxalocrotonase tautomerase isozyme
B: 4-oxalocrotonase tautomerase isozyme


Theoretical massNumber of molelcules
Total (without water)15,2052
Polymers15,2052
Non-polymers00
Water66737
1
A: 4-oxalocrotonase tautomerase isozyme
B: 4-oxalocrotonase tautomerase isozyme

A: 4-oxalocrotonase tautomerase isozyme
B: 4-oxalocrotonase tautomerase isozyme

A: 4-oxalocrotonase tautomerase isozyme
B: 4-oxalocrotonase tautomerase isozyme


Theoretical massNumber of molelcules
Total (without water)45,6166
Polymers45,6166
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
Buried area13100 Å2
ΔGint-82 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.236, 50.236, 158.078
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-117-

HOH

21A-120-

HOH

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Components

#1: Protein 4-oxalocrotonase tautomerase isozyme


Mass: 7602.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylibium petroleiphilum (bacteria) / Strain: PM1 / Gene: Mpe_A3323 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A2SL37, oxaloacetate tautomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.89 Å3/Da / Density % sol: 35.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 4.3 M Sodium Formate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 4, 2011
RadiationMonochromator: Optics mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→158.08 Å / Num. all: 15338 / Num. obs: 15338 / % possible obs: 99.8 %
Reflection shellResolution: 1.64→1.683 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→158.08 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.016 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26306 748 5 %RANDOM
Rwork0.22564 ---
all0.22739 14319 --
obs0.22739 14319 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.052 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.64→158.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 0 37 998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.019967
X-RAY DIFFRACTIONr_angle_refined_deg2.3191.951307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.25423.91346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03215176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9931512
X-RAY DIFFRACTIONr_chiral_restr0.1640.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02706
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 43 -
Rwork0.316 849 -
obs--94.29 %

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