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- PDB-9nf4: Cg10062 E114N mutant apo -

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Basic information

Entry
Database: PDB / ID: 9nf4
TitleCg10062 E114N mutant apo
Components4-oxalocrotonate tautomerase
KeywordsHYDROLASE / Cg10062 / Tautomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 4-oxalocrotonate tautomerase
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cg10062 E114N mutant apo
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionFeb 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,17712
Polymers102,6016
Non-polymers5766
Water3,189177
1
A: 4-oxalocrotonate tautomerase
B: 4-oxalocrotonate tautomerase
C: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5896
Polymers51,3013
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-108 kcal/mol
Surface area17390 Å2
MethodPISA
2
D: 4-oxalocrotonate tautomerase
E: 4-oxalocrotonate tautomerase
F: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5896
Polymers51,3013
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-107 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.555, 88.834, 81.655
Angle α, β, γ (deg.)90.000, 100.058, 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

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Components

#1: Protein
4-oxalocrotonate tautomerase


Mass: 17100.182 Da / Num. of mol.: 6 / Mutation: E114N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: AUP69_07050, AUP70_06515 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S2T163
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulfate 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.13 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 35409 / % possible obs: 96.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 33.47 Å2 / Rpim(I) all: 0.1 / Net I/σ(I): 7.19
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 1774 / Rpim(I) all: 0.339

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→30.31 Å / SU ML: 0.4436 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.4822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3081 2811 5.88 %
Rwork0.2134 44972 -
obs0.2189 33933 66.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.55 Å2
Refinement stepCycle: LAST / Resolution: 2.51→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 30 177 7374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00947367
X-RAY DIFFRACTIONf_angle_d1.166710000
X-RAY DIFFRACTIONf_chiral_restr0.05811093
X-RAY DIFFRACTIONf_plane_restr0.01011292
X-RAY DIFFRACTIONf_dihedral_angle_d20.9642770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.560.3573710.32441169X-RAY DIFFRACTION34.3
2.56-2.60.4113940.29911492X-RAY DIFFRACTION43.85
2.6-2.650.3952990.29031564X-RAY DIFFRACTION46.78
2.65-2.710.3551040.26641660X-RAY DIFFRACTION48.36
2.71-2.770.35781050.281691X-RAY DIFFRACTION49.63
2.77-2.830.36051110.27431744X-RAY DIFFRACTION51.89
2.83-2.90.36261150.25061899X-RAY DIFFRACTION55.09
2.9-2.980.30221210.241961X-RAY DIFFRACTION58.81
2.98-3.070.33221380.23822251X-RAY DIFFRACTION65.27
3.07-3.170.31111470.21342409X-RAY DIFFRACTION69.32
3.17-3.280.38261560.24092439X-RAY DIFFRACTION72.59
3.28-3.410.36111620.23332483X-RAY DIFFRACTION73.53
3.41-3.570.30191440.20972315X-RAY DIFFRACTION68.31
3.57-3.750.37591470.22392278X-RAY DIFFRACTION67.76
3.75-3.990.271680.20012787X-RAY DIFFRACTION81.49
3.99-4.30.29451770.18282866X-RAY DIFFRACTION83.9
4.3-4.730.26491670.17262629X-RAY DIFFRACTION78.63
4.73-5.410.24081820.18152858X-RAY DIFFRACTION83.89
5.41-6.80.30282050.20073264X-RAY DIFFRACTION95.22
6.8-30.310.27981980.2043213X-RAY DIFFRACTION94.57

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