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- PDB-6ogm: Crystal structure of apo unFused 4-OT -

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Basic information

Entry
Database: PDB / ID: 6ogm
TitleCrystal structure of apo unFused 4-OT
Components(4-oxalocrotonate tautomerase) x 2
KeywordsHYDROLASE
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / isomerase activity / 2-Layer Sandwich / Alpha Beta / 4-oxalocrotonate tautomerase
Function and homology information
Biological speciesBurkholderia lata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.865 Å
AuthorsMedellin, B.P. / Whitman, C.P. / Zhang, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM-129331 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.
Authors: Baas, B.J. / Medellin, B.P. / LeVieux, J.A. / de Ruijter, M. / Zhang, Y.J. / Brown, S.D. / Akiva, E. / Babbitt, P.C. / Whitman, C.P.
History
DepositionApr 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-oxalocrotonate tautomerase
B: 4-oxalocrotonate tautomerase
C: 4-oxalocrotonate tautomerase
D: 4-oxalocrotonate tautomerase
E: 4-oxalocrotonate tautomerase
F: 4-oxalocrotonate tautomerase
G: 4-oxalocrotonate tautomerase
H: 4-oxalocrotonate tautomerase
I: 4-oxalocrotonate tautomerase
J: 4-oxalocrotonate tautomerase
K: 4-oxalocrotonate tautomerase
L: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,55914
Polymers79,37512
Non-polymers1842
Water7,332407
1
A: 4-oxalocrotonate tautomerase
B: 4-oxalocrotonate tautomerase
C: 4-oxalocrotonate tautomerase
D: 4-oxalocrotonate tautomerase
E: 4-oxalocrotonate tautomerase
F: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8728
Polymers39,6886
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-90 kcal/mol
Surface area13010 Å2
MethodPISA
2
G: 4-oxalocrotonate tautomerase
H: 4-oxalocrotonate tautomerase
I: 4-oxalocrotonate tautomerase
J: 4-oxalocrotonate tautomerase
K: 4-oxalocrotonate tautomerase
L: 4-oxalocrotonate tautomerase


Theoretical massNumber of molelcules
Total (without water)39,6886
Polymers39,6886
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13690 Å2
ΔGint-95 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.628, 81.570, 96.231
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-oxalocrotonate tautomerase / unFused 4-OT


Mass: 6638.694 Da / Num. of mol.: 6 / Fragment: Subunit beta (UNP residues 67-128)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383) (bacteria)
Strain: ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383
Gene: Bcep18194_B2498
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q392K7
#2: Protein
4-oxalocrotonate tautomerase / unFused 4-OT


Mass: 6590.475 Da / Num. of mol.: 6 / Fragment: Subunit alpha (UNP residues 2-66)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383) (bacteria)
Strain: ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383
Gene: Bcep18194_B2498
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q392K7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 200 mM magnesium acetate, 28% PEG3550 / 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: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2018
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.86→47.88 Å / Num. obs: 50873 / % possible obs: 97.38 % / Redundancy: 3.6 % / CC1/2: 0.991 / Rpim(I) all: 0.07 / Rsym value: 0.117 / Net I/σ(I): 9.54
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 17024 / CC1/2: 0.726 / Rpim(I) all: 0.313 / Rsym value: 0.511 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000v1.0data reduction
HKL-2000v1.0data scaling
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BLM

6blm


Resolution: 1.865→47.88 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.37
RfactorNum. reflection% reflection
Rfree0.2295 2000 4.04 %
Rwork0.1818 --
obs0.1837 49505 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.865→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5252 0 12 407 5671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075317
X-RAY DIFFRACTIONf_angle_d0.9217213
X-RAY DIFFRACTIONf_dihedral_angle_d5.4353257
X-RAY DIFFRACTIONf_chiral_restr0.052917
X-RAY DIFFRACTIONf_plane_restr0.007931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8646-1.91120.30811310.24813133X-RAY DIFFRACTION91
1.9112-1.96290.28531420.22313371X-RAY DIFFRACTION97
1.9629-2.02060.26751420.20023357X-RAY DIFFRACTION97
2.0206-2.08580.25671410.19373358X-RAY DIFFRACTION96
2.0858-2.16040.23581420.19173371X-RAY DIFFRACTION98
2.1604-2.24690.25971420.1923362X-RAY DIFFRACTION97
2.2469-2.34910.24391410.18273365X-RAY DIFFRACTION97
2.3491-2.4730.22681440.18193425X-RAY DIFFRACTION98
2.473-2.62790.22961440.18493408X-RAY DIFFRACTION99
2.6279-2.83080.23051460.18383444X-RAY DIFFRACTION98
2.8308-3.11560.23391430.18673416X-RAY DIFFRACTION99
3.1156-3.56630.21711470.17533476X-RAY DIFFRACTION99
3.5663-4.49270.20251460.15263477X-RAY DIFFRACTION99
4.4927-47.89740.2131490.18263542X-RAY DIFFRACTION99

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