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- PDB-9ngh: Cg10062 E114N mutant with acetylenecarboxylic acid -

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Basic information

Entry
Database: PDB / ID: 9ngh
TitleCg10062 E114N mutant with acetylenecarboxylic acid
Components4-oxalocrotonate tautomerase
KeywordsHYDROLASE / Tautomerase / Cg10062 / acetylenecaarboxylic acid
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: 2.92 Å
AuthorsSilva, K. / Nayebi, G.H. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cg10062 E114N mutant with acetylenecarboxylic acid
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionFeb 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9982
Polymers16,9281
Non-polymers701
Water21612
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)50,9946
Polymers50,7843
Non-polymers2103
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8060 Å2
ΔGint-38 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.162, 146.162, 146.162
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


Mass: 16927.951 Da / Num. of mol.: 1 / 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-A1BXY / prop-2-ynoic acid


Mass: 70.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 2% v/v TacsimateTM pH 5.0 5% 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: 0.98 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 17302 / % possible obs: 99.8 % / Redundancy: 10.2 % / Biso Wilson estimate: 51.68 Å2 / Rpim(I) all: 0.056 / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 843 / Rpim(I) all: 0.664

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→35.45 Å / SU ML: 0.4137 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3117 1959 9.95 %
Rwork0.2519 17721 -
obs0.2579 10828 89.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.02 Å2
Refinement stepCycle: LAST / Resolution: 2.92→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 5 12 1194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121231
X-RAY DIFFRACTIONf_angle_d1.20651672
X-RAY DIFFRACTIONf_chiral_restr0.0572183
X-RAY DIFFRACTIONf_plane_restr0.0064218
X-RAY DIFFRACTIONf_dihedral_angle_d31.8911165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.990.2987650.2492593X-RAY DIFFRACTION41.23
2.99-3.070.32291170.24151077X-RAY DIFFRACTION77.18
3.07-3.160.32711480.24131320X-RAY DIFFRACTION92.15
3.16-3.260.30451430.23471314X-RAY DIFFRACTION94.92
3.26-3.380.2781530.24541374X-RAY DIFFRACTION94.79
3.38-3.510.31141400.26631283X-RAY DIFFRACTION91.28
3.51-3.670.36921470.29521373X-RAY DIFFRACTION96.39
3.67-3.870.33181510.25531356X-RAY DIFFRACTION97.1
3.87-4.110.34871510.23081367X-RAY DIFFRACTION96.81
4.11-4.420.23941560.22491384X-RAY DIFFRACTION97.35
4.43-4.870.26031550.21621358X-RAY DIFFRACTION96.06
4.87-5.570.34471500.22651363X-RAY DIFFRACTION95.58
5.57-7.010.34341450.27821305X-RAY DIFFRACTION92.71
7.02-35.450.32381380.2981254X-RAY DIFFRACTION87.82

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