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- PDB-6vvm: R7 fused 4-OT wild type asymmetric trimer -

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Basic information

Entry
Database: PDB / ID: 6vvm
TitleR7 fused 4-OT wild type asymmetric trimer
Components4-oxalocrotonate tautomerase family enzyme
KeywordsISOMERASE / asymmetric / fused / 4-oxalocrotonate tautomerase
Function / homology4-oxalocrotonate tautomerase family enzyme / 4-oxalocrotonate tautomerase family enzyme
Function and homology information
Biological speciesBurkholderia sp. RPE67 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsMedellin, B.P. / Whitman, C.P. / Zhang, Y.J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-129331 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-41239 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-104896 United States
Robert A. Welch FoundationF-1334 United States
Robert A. Welch FoundationF-1778 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer.
Authors: Medellin, B.P. / Lancaster, E.B. / Brown, S.D. / Rakhade, S. / Babbitt, P.C. / Whitman, C.P. / Zhang, Y.J.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-oxalocrotonate tautomerase family enzyme
B: 4-oxalocrotonate tautomerase family enzyme
C: 4-oxalocrotonate tautomerase family enzyme


Theoretical massNumber of molelcules
Total (without water)38,4083
Polymers38,4083
Non-polymers00
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-31 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.714, 49.957, 48.028
Angle α, β, γ (deg.)90.000, 100.540, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-265-

HOH

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Components

#1: Protein 4-oxalocrotonate tautomerase family enzyme


Mass: 12802.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. RPE67 (bacteria) / Gene: BRPE67_ACDS14250
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A060NYR7, UniProt: A0A7U6GPC9*PLUS, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 15-30% PEG5000 MME / PH range: 6-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.83→47.22 Å / Num. obs: 29709 / % possible obs: 97.1 % / Redundancy: 3.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.1314 / Rpim(I) all: 0.0783 / Net I/σ(I): 8.2
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 2277 / CC1/2: 0.79 / % possible all: 76

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Processing

Software
NameVersionClassification
PHENIX1.16.1refinement
HKL-20001data reduction
HKL-20001data scaling
MOLREP1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BLM

6blm


Resolution: 1.83→47.22 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2285 --
Rwork0.1869 --
obs-29709 97.1 %
Displacement parametersBiso mean: 29.59 Å2
Refinement stepCycle: LAST / Resolution: 1.83→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 0 362 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872730
X-RAY DIFFRACTIONf_angle_d0.93713714
X-RAY DIFFRACTIONf_chiral_restr0.056471
X-RAY DIFFRACTIONf_plane_restr0.0052477
X-RAY DIFFRACTIONf_dihedral_angle_d18.75481695
LS refinement shellResolution: 1.83→1.9 Å
RfactorNum. reflection
Rfree0.2918 -
Rwork0.2527 -
obs-2277

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