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- PDB-7ms8: Crystal structure of Y103F mutant of Cg10062 with a covalent inte... -

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Basic information

Entry
Database: PDB / ID: 7ms8
TitleCrystal structure of Y103F mutant of Cg10062 with a covalent intermediate of the hydration of acetylenecarboxylic acid
Components4-oxalocrotonate tautomerase
KeywordsISOMERASE / 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: 2.5 Å
AuthorsNayebi, G.H. / Geiger, J.H. / Draths, K.
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 30, 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

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Assembly

Deposited unit
A: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1122
Polymers19,0221
Non-polymers901
Water37821
1
A: 4-oxalocrotonate tautomerase
hetero molecules

A: 4-oxalocrotonate tautomerase
hetero molecules

A: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3376
Polymers57,0673
Non-polymers2703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9060 Å2
ΔGint-36 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.684, 146.684, 146.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

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Components

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


Mass: 19022.250 Da / Num. of mol.: 1 / Mutation: Y103F
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.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 6.91 Å3/Da / Density % sol: 82.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM magnesium acetate tetrahydrate, 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: 2.5→33.65 Å / Num. obs: 19222 / % possible obs: 99.84 % / Redundancy: 10.4 % / Biso Wilson estimate: 56.68 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.033 / Rrim(I) all: 0.108 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 1895 / Rpim(I) all: 0.482

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7MS0

7ms0


Resolution: 2.5→33.65 Å / SU ML: 0.3241 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2505 1931 10 %
Rwork0.2182 17376 -
obs0.2213 19220 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 5 21 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591231
X-RAY DIFFRACTIONf_angle_d0.90171668
X-RAY DIFFRACTIONf_chiral_restr0.0634182
X-RAY DIFFRACTIONf_plane_restr0.004216
X-RAY DIFFRACTIONf_dihedral_angle_d35.6263466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.33191360.29921221X-RAY DIFFRACTION100
2.56-2.630.30451330.30981199X-RAY DIFFRACTION100
2.63-2.710.30111350.28951217X-RAY DIFFRACTION100
2.71-2.790.32781340.28671205X-RAY DIFFRACTION100
2.79-2.890.30141360.28451230X-RAY DIFFRACTION100
2.89-3.010.26911370.26161222X-RAY DIFFRACTION99.93
3.01-3.140.28581350.23781214X-RAY DIFFRACTION100
3.15-3.310.25321360.22131228X-RAY DIFFRACTION100
3.31-3.520.23191380.2071236X-RAY DIFFRACTION100
3.52-3.790.25081360.20841232X-RAY DIFFRACTION99.93
3.79-4.170.20431400.18681254X-RAY DIFFRACTION100
4.17-4.770.18491390.16081253X-RAY DIFFRACTION99.07
4.77-60.22931420.1921276X-RAY DIFFRACTION100
6.01-33.650.30571540.24361389X-RAY DIFFRACTION100

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