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- PDB-3n4h: Crystal structure of Cg10062 inactivated by (S)-oxirane-2-carboxylate -

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Basic information

Entry
Database: PDB / ID: 3n4h
TitleCrystal structure of Cg10062 inactivated by (S)-oxirane-2-carboxylate
ComponentsPutative tautomerase
KeywordsHYDROLASE / Cg10062 / cis-3-Chloroacrylic Acid Dehalogenase / Tautomerase superfamily / Beta-alpha-beta motif
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 / Tautomerase cis-CaaD-like domain-containing protein
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGuo, Y. / Robertson, B.A. / Hackert, M.L. / Whitman, C.P.
CitationJournal: To be Published
Title: Crystal Structures of the Native and Inactivated Cg10062, a cis-3-Chloroacrylic Acid Dehalogenase from Corynebacterium glutamicum: Implications for the Evolution of cis-3-Chloroacrylic Acid ...Title: Crystal Structures of the Native and Inactivated Cg10062, a cis-3-Chloroacrylic Acid Dehalogenase from Corynebacterium glutamicum: Implications for the Evolution of cis-3-Chloroacrylic Acid Dehalogenase Activity in the Tautomerase Superfamily
Authors: Guo, Y. / Robertson, B.A. / J Poelarends, G. / Thunnissen, A.-M.W.H. / Hackert, M.L. / Whitman, C.P. / Dijkstra, B.W.
History
DepositionMay 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Database references / Category: citation_author / pdbx_unobs_or_zero_occ_atoms / Item: _citation_author.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)17,2031
Polymers17,2031
Non-polymers00
Water1,874104
1
A: Putative tautomerase

A: Putative tautomerase

A: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)51,6103
Polymers51,6103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area6620 Å2
ΔGint-37 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.435, 49.435, 80.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

21A-225-

HOH

31A-226-

HOH

41A-239-

HOH

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Components

#1: Protein Putative tautomerase / Putative uncharacterized protein Cgl0062


Mass: 17203.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg0081, Cg10062, Cgl0062 / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: Q8NU77, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 1.64 Å3/Da / Density % sol: 25.18 %
Crystal growTemperature: 298 K / pH: 4
Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (3% PEG 6000, pH 4.0) and protein solution (18.1mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), vapor diffusion, ...Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (3% PEG 6000, pH 4.0) and protein solution (18.1mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 4, 2005
RadiationMonochromator: BLUE MAX-FLUX OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 7841 / % possible obs: 99.8 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 64.887
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 8.6 / Num. unique all: 766 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N4G

3n4g


Resolution: 2.02→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.932 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 362 4.6 %RANDOM
Rwork0.166 ---
obs0.169 7835 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.23 Å2 / Biso mean: 35.552 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.02→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 104 1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022994
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9431350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.8915116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28223.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82215172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.478158
X-RAY DIFFRACTIONr_chiral_restr0.1220.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02746
X-RAY DIFFRACTIONr_nbd_refined0.2680.2486
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3550.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.231
X-RAY DIFFRACTIONr_mcbond_it1.4071.5615
X-RAY DIFFRACTIONr_mcangle_it2.1352962
X-RAY DIFFRACTIONr_scbond_it3.663444
X-RAY DIFFRACTIONr_scangle_it4.7554.5388
X-RAY DIFFRACTIONr_rigid_bond_restr3.27131059
X-RAY DIFFRACTIONr_sphericity_free4.943130
X-RAY DIFFRACTIONr_sphericity_bonded3.2283973
LS refinement shellResolution: 2.02→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 33 -
Rwork0.159 535 -
all-568 -
obs--100 %

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