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- PDB-6vvw: W0 fused 4-OT wild type symmetric trimer -

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Basic information

Entry
Database: PDB / ID: 6vvw
TitleW0 fused 4-OT wild type symmetric trimer
ComponentsTautomerase
KeywordsISOMERASE / symmetric / fused / 4-oxalocrotonate tautomerase
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / : / Tautomerase/MIF superfamily / isomerase activity / Putative tautomerase
Function and homology information
Biological speciesAdvenella mimigardefordensis DPN7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Tautomerase
B: Tautomerase
C: Tautomerase
D: Tautomerase
E: Tautomerase
F: Tautomerase
G: Tautomerase
H: Tautomerase


Theoretical massNumber of molelcules
Total (without water)109,4938
Polymers109,4938
Non-polymers00
Water1,13563
1
A: Tautomerase

A: Tautomerase

A: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area7480 Å2
ΔGint-26 kcal/mol
Surface area13680 Å2
MethodPISA
2
B: Tautomerase

B: Tautomerase

B: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7460 Å2
ΔGint-26 kcal/mol
Surface area13080 Å2
MethodPISA
3
C: Tautomerase

C: Tautomerase

C: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7260 Å2
ΔGint-25 kcal/mol
Surface area13910 Å2
MethodPISA
4
D: Tautomerase

D: Tautomerase

D: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area7760 Å2
ΔGint-24 kcal/mol
Surface area13330 Å2
MethodPISA
5
E: Tautomerase

E: Tautomerase

E: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7400 Å2
ΔGint-26 kcal/mol
Surface area13710 Å2
MethodPISA
6
F: Tautomerase

F: Tautomerase

F: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area7440 Å2
ΔGint-21 kcal/mol
Surface area13430 Å2
MethodPISA
7
G: Tautomerase

G: Tautomerase

G: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area7350 Å2
ΔGint-25 kcal/mol
Surface area13880 Å2
MethodPISA
8
H: Tautomerase

H: Tautomerase

H: Tautomerase


Theoretical massNumber of molelcules
Total (without water)41,0603
Polymers41,0603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7630 Å2
ΔGint-20 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.866, 83.866, 149.604
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Tautomerase


Mass: 13686.604 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Advenella mimigardefordensis DPN7 (bacteria)
Gene: MIM_c08740
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: W0PD56, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 27-37% PEG5000 MME / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2019
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.45
ReflectionResolution: 2.1→41.93 Å / Num. obs: 68347 / % possible obs: 99.5 % / Redundancy: 5.4 % / CC1/2: 0.992 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.17 Å / Num. unique obs: 6690 / CC1/2: 0.75 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UNQ

5unq


Resolution: 2.1→41.93 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3335 --
Rwork0.275 --
obs-68347 99.5 %
Displacement parametersBiso max: 35.7 Å2 / Biso mean: 21.6767 Å2 / Biso min: 9.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 0 63 7301
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection
Rfree0.3578 -
Rwork0.3102 -
obs-6690

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