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

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Basic information

Entry
Database: PDB / ID: 4faz
TitleKinetic and structural characterization of the 4-oxalocrotonate tautomerase isozymes from Methylibium petroleiphilum
Components4-oxalocrotonate isomerase protein
KeywordsISOMERASE / alpha/beta fold / Tautomerase
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: 1.57 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 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-oxalocrotonate isomerase protein
B: 4-oxalocrotonate isomerase protein
C: 4-oxalocrotonate isomerase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8384
Polymers20,7423
Non-polymers961
Water1,09961
1
A: 4-oxalocrotonate isomerase protein
B: 4-oxalocrotonate isomerase protein
C: 4-oxalocrotonate isomerase protein
hetero molecules

A: 4-oxalocrotonate isomerase protein
B: 4-oxalocrotonate isomerase protein
C: 4-oxalocrotonate isomerase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6768
Polymers41,4846
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13850 Å2
ΔGint-112 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.170, 76.169, 69.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 4-oxalocrotonate isomerase protein


Mass: 6913.975 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylibium petroleiphilum (bacteria) / Strain: PM1 / Gene: Mpe_A2265 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A2SI32, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM tri-Ammonium Citrate, 10% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→47.22 Å / Num. all: 24295 / Num. obs: 20889 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.57→1.61 Å / % possible all: 98.5

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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
Starting model: PDB entry 1BJP

1bjp


Resolution: 1.57→47.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.955 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27466 1140 5.2 %RANDOM
Rwork0.22881 ---
all0.23103 24295 --
obs0.23103 20889 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---0.9 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.57→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 5 61 1523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191488
X-RAY DIFFRACTIONr_angle_refined_deg2.1491.9432005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20324.09166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27515270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2661512
X-RAY DIFFRACTIONr_chiral_restr0.1630.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211103
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 87 -
Rwork0.429 1345 -
obs--91.33 %

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