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- PDB-9nf6: Cg10062 E114N mutant with a covalent hydroxypropionate and acryla... -

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Basic information

Entry
Database: PDB / ID: 9nf6
TitleCg10062 E114N mutant with a covalent hydroxypropionate and acrylate intermediate of the hydration of acetylenecarboxylic acid
Components4-oxalocrotonate tautomerase
KeywordsHYDROLASE / Cg10062 / Tautomerase / acetylenecarboxylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 3-HYDROXY-PROPANOIC ACID / ACRYLIC ACID / 4-oxalocrotonate tautomerase
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cg10062 E114N mutant with a covalent hydroxypropionate and acrylate intermediate of the hydration of acetylenecarboxylic acid
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)103,14712
Polymers102,6016
Non-polymers5466
Water1,45981
1
A: 4-oxalocrotonate tautomerase
D: 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 area9250 Å2
ΔGint-102 kcal/mol
Surface area17370 Å2
MethodPISA
2
B: 4-oxalocrotonate tautomerase
C: 4-oxalocrotonate tautomerase
E: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5596
Polymers51,3013
Non-polymers2583
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-61 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.396, 88.062, 79.318
Angle α, β, γ (deg.)90.000, 100.339, 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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#4: Chemical ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
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: 2.6→40 Å / Num. obs: 29108 / % possible obs: 96.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 41.93 Å2 / Rpim(I) all: 0.101 / Net I/σ(I): 8.8
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 1475 / Rpim(I) all: 0.459

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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: 2.63→33.49 Å / SU ML: 0.3952 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.4325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2928 3124 7.75 %
Rwork0.1941 37209 -
obs0.2018 25850 67.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.68 Å2
Refinement stepCycle: LAST / Resolution: 2.63→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7182 0 31 81 7294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00977363
X-RAY DIFFRACTIONf_angle_d1.1629985
X-RAY DIFFRACTIONf_chiral_restr0.05751093
X-RAY DIFFRACTIONf_plane_restr0.01041289
X-RAY DIFFRACTIONf_dihedral_angle_d20.25632769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.670.3368400.2726461X-RAY DIFFRACTION18.28
2.68-2.720.3187560.2518619X-RAY DIFFRACTION24.98
2.72-2.770.3635620.2541766X-RAY DIFFRACTION30.54
2.77-2.820.3797740.2735872X-RAY DIFFRACTION35.02
2.82-2.870.3245850.27771023X-RAY DIFFRACTION40.84
2.87-2.930.33731030.25791245X-RAY DIFFRACTION47.99
2.93-2.990.41811060.24831317X-RAY DIFFRACTION53.84
2.99-3.060.32821380.23331554X-RAY DIFFRACTION61.19
3.06-3.140.33721450.2221711X-RAY DIFFRACTION67.52
3.14-3.220.30741490.21361815X-RAY DIFFRACTION73.5
3.22-3.320.3141620.2051961X-RAY DIFFRACTION77.62
3.32-3.420.3041750.1942097X-RAY DIFFRACTION82.32
3.42-3.550.29631840.19342175X-RAY DIFFRACTION87.24
3.55-3.690.25751870.17372277X-RAY DIFFRACTION89.67
3.69-3.860.29541920.19122312X-RAY DIFFRACTION91.45
3.86-4.060.30381890.18422201X-RAY DIFFRACTION89.21
4.06-4.310.30871800.17442089X-RAY DIFFRACTION82.84
4.31-4.650.27791480.18131699X-RAY DIFFRACTION67.14
4.65-5.110.25761760.16892039X-RAY DIFFRACTION81.05
5.11-5.850.26211810.19132205X-RAY DIFFRACTION87.4
5.85-7.350.32151950.21222399X-RAY DIFFRACTION94.91
7.36-33.490.24451970.16872372X-RAY DIFFRACTION94.55

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