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- PDB-2op8: Crystal Structure of YwhB- Homologue of 4-Oxalocrotonate Tautomerase -

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Basic information

Entry
Database: PDB / ID: 2op8
TitleCrystal Structure of YwhB- Homologue of 4-Oxalocrotonate Tautomerase
ComponentsProbable tautomerase ywhB
KeywordsISOMERASE / 4-OT / tautomerase
Function / homology
Function and homology information


2-hydroxymuconate tautomerase / 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
2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHackert, M.L. / Whitman, C.P. / Almrud, J.J.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of YwhB, a 4-Oxalocrotonate Tautomerase Homologue from Bacillus subtilis: The Structural Basis for Catalysis, Inhibition, and Reaction Stereoselectivity
Authors: Hackert, M.L. / Whitman, C.P. / Almrud, J.J. / Dasgupta, R. / Wang, S.C. / Johnson, W.H.
History
DepositionJan 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Probable tautomerase ywhB
B: Probable tautomerase ywhB


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers14,0522
Non-polymers00
Water86548
1
A: Probable tautomerase ywhB
B: Probable tautomerase ywhB

A: Probable tautomerase ywhB
B: Probable tautomerase ywhB

A: Probable tautomerase ywhB
B: Probable tautomerase ywhB


Theoretical massNumber of molelcules
Total (without water)42,1566
Polymers42,1566
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12430 Å2
ΔGint-50 kcal/mol
Surface area16110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)141.800, 141.800, 141.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-86-

HOH

21A-88-

HOH

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Components

#1: Protein Probable tautomerase ywhB


Mass: 7026.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ywhB / Plasmid: pET-24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS
References: UniProt: P70994, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: protein (25 mg/ml) buffered in 50 mM HEPES, pH 7.3, 5uL of protein solution mixed with 5uL of 50% methyl-pentanediol (MPD), 0.2M (NH4)H2PO4, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.30

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 8746 / % possible obs: 99.9 % / Redundancy: 68.27 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.086 / Net I/σ(I): 21.5
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 6 / Rsym value: 0.483 / % possible all: 0.9

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJP

1bjp


Resolution: 2.5→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.237 413 -RANDOM
Rwork0.218 ---
obs0.218 8624 100 %-
all-8737 --
Displacement parametersBiso mean: 41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 0 48 1005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.038
RfactorNum. reflection% reflection
Rfree0.246 43 -
Rwork0.276 --
obs--100 %

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