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- PDB-7ms9: Crystal structure of E114D mutant of Cg10062 with a covalent inte... -

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Basic information

Entry
Database: PDB / ID: 7ms9
TitleCrystal structure of E114D mutant of Cg10062 with a covalent intermediate of the hydration of acetylenecarboxylic acid
Components4-oxalocrotonate tautomerase
KeywordsHYDROLASE / tautomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / 3-HYDROXY-PROPANOIC ACID / 4-oxalocrotonate tautomerase
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNayebi, G.H. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2021
Title: Cg10062 Catalysis Forges a Link between Acetylenecarboxylic Acid and Bacterial Metabolism.
Authors: Mathes Hewage, A. / Nayebi Gavgani, H. / Chi, D. / Qiu, B. / Geiger, J.H. / Draths, K.
History
DepositionMay 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)229,41424
Polymers228,29112
Non-polymers1,12312
Water4,954275
1
A: 4-oxalocrotonate tautomerase
B: 4-oxalocrotonate tautomerase
C: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3496
Polymers57,0733
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-65 kcal/mol
Surface area14280 Å2
MethodPISA
2
D: 4-oxalocrotonate tautomerase
E: 4-oxalocrotonate tautomerase
F: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3616
Polymers57,0733
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-111 kcal/mol
Surface area14350 Å2
MethodPISA
3
G: 4-oxalocrotonate tautomerase
H: 4-oxalocrotonate tautomerase
I: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3496
Polymers57,0733
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-63 kcal/mol
Surface area14410 Å2
MethodPISA
4
J: 4-oxalocrotonate tautomerase
K: 4-oxalocrotonate tautomerase
L: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3556
Polymers57,0733
Non-polymers2823
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-88 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.319, 146.299, 146.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
4-oxalocrotonate tautomerase / Cis-3-chloroacrylic acid dehalogenase


Mass: 19024.223 Da / Num. of mol.: 12 / Mutation: E114D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria)
Gene: APT58_00490, AUO95_07180, CS176_0056, FM102_14895, KaCgl_17770, KbCgl_30240
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0S2T163, 2-hydroxymuconate tautomerase
#2: Chemical
ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM potassium sulfate, 10% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→36.09 Å / Num. obs: 116532 / % possible obs: 99.47 % / Redundancy: 6.4 % / Biso Wilson estimate: 46.89 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.05 / Rrim(I) all: 0.127 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 11226 / Rpim(I) all: 0.826

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7MS0

7ms0


Resolution: 2.2→36.09 Å / SU ML: 0.2813 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 2004 1.72 %
Rwork0.183 114466 -
obs0.1839 116470 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11820 0 60 275 12155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002612493
X-RAY DIFFRACTIONf_angle_d0.5817006
X-RAY DIFFRACTIONf_chiral_restr0.0451895
X-RAY DIFFRACTIONf_plane_restr0.00512190
X-RAY DIFFRACTIONf_dihedral_angle_d18.44614691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.28731330.28437593X-RAY DIFFRACTION93.46
2.26-2.320.31741410.27328124X-RAY DIFFRACTION99.89
2.32-2.380.32741430.26188175X-RAY DIFFRACTION99.98
2.38-2.460.25631420.25448114X-RAY DIFFRACTION100
2.46-2.550.29591450.24748168X-RAY DIFFRACTION100
2.55-2.650.30731420.23538144X-RAY DIFFRACTION99.94
2.65-2.770.31951430.23598157X-RAY DIFFRACTION99.87
2.77-2.920.28121410.22848196X-RAY DIFFRACTION99.65
2.92-3.10.26851420.22998162X-RAY DIFFRACTION99.92
3.1-3.340.27431440.20498227X-RAY DIFFRACTION100
3.34-3.680.22171440.17618234X-RAY DIFFRACTION99.93
3.68-4.210.20291450.15028278X-RAY DIFFRACTION99.87
4.21-5.30.15831490.1238317X-RAY DIFFRACTION99.71
5.3-100.23511500.15848577X-RAY DIFFRACTION99.53

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