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- PDB-3n4d: Crystal structure of Cg10062 inactivated by(R)-oxirane-2-carboxylate -

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Basic information

Entry
Database: PDB / ID: 3n4d
TitleCrystal structure of Cg10062 inactivated by(R)-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: 2.54 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: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...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 / 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

Downloads & links

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Assembly

Deposited unit
A: Putative tautomerase
B: Putative tautomerase
C: Putative tautomerase
D: Putative tautomerase
E: Putative tautomerase
F: Putative tautomerase
G: Putative tautomerase
H: Putative tautomerase
I: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)154,8299
Polymers154,8299
Non-polymers00
Water8,647480
1
A: Putative tautomerase
B: Putative tautomerase
C: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)51,6103
Polymers51,6103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-41 kcal/mol
Surface area17170 Å2
MethodPISA
2
D: Putative tautomerase
E: Putative tautomerase
F: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)51,6103
Polymers51,6103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-42 kcal/mol
Surface area16890 Å2
MethodPISA
3
G: Putative tautomerase
H: Putative tautomerase
I: Putative tautomerase


Theoretical massNumber of molelcules
Total (without water)51,6103
Polymers51,6103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-38 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.099, 131.002, 179.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative tautomerase / Putative uncharacterized protein Cgl0062


Mass: 17203.256 Da / Num. of mol.: 9 / Fragment: Cg10062
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.: 480 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 298 K / pH: 4
Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (0.07 M sodium aetate buffer, pH 4.6, 1.4 M sodium chloride) and protein solution (18.9mg/L Cg10062 in 10mM ...Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (0.07 M sodium aetate buffer, pH 4.6, 1.4 M sodium chloride) and protein solution (18.9mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), Hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 7, 2005
RadiationMonochromator: BLUE MAX-FLUX OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 89329 / % possible obs: 99.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 61.2
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.206 / % possible all: 99.9

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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 2FLT

2flt


Resolution: 2.54→45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24327 2312 5.1 %RANDOM
Rwork0.22343 ---
obs0.22446 43020 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.54→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10546 0 0 480 11026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.95814651
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.14351283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.32623.97534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.312151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.691589
X-RAY DIFFRACTIONr_chiral_restr0.0890.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028194
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3050.26221
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.27405
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3220.2695
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3931.56506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.551210503
X-RAY DIFFRACTIONr_scbond_it2.1634284
X-RAY DIFFRACTIONr_scangle_it3.264.54148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 183 -
Rwork0.325 3133 -
obs--100 %

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