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- PDB-3gm5: Crystal structure of a putative methylmalonyl-coenzyme A epimeras... -

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Basic information

Entry
Database: PDB / ID: 3gm5
TitleCrystal structure of a putative methylmalonyl-coenzyme A epimerase from Thermoanaerobacter tengcongensis at 2.0 A resolution
ComponentsLactoylglutathione lyase and related lyases
KeywordsISOMERASE / sheet-helix-sheet-sheet-sheet motif
Function / homology
Function and homology information


Methylmalonyl-CoA epimerase / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Lactoylglutathione lyase and related lyases
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLiang, D.-C. / Shi, L. / Gao, P. / Yan, X.-X.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of a putative methylmalonyl-coenzyme a epimerase from Thermoanaerobacter tengcongensis at 2.0 A resolution
Authors: Shi, L. / Gao, P. / Yan, X.-X. / Liang, D.-C.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactoylglutathione lyase and related lyases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1654
Polymers18,7801
Non-polymers3843
Water2,270126
1
A: Lactoylglutathione lyase and related lyases
hetero molecules

A: Lactoylglutathione lyase and related lyases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3298
Polymers37,5612
Non-polymers7686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3980 Å2
ΔGint-81 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.022, 54.022, 104.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lactoylglutathione lyase and related lyases / putative methylmalonyl-coenzyme A epimerase


Mass: 18780.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Thermoanaerobacter tengcongensis
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: GloA, TTE0360 / Plasmid: pHAT-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RCQ6, methylmalonyl-CoA epimerase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.6
Details: 0.1M citric acid, pH 2.6, 1.6M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jan 18, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 11130 / Num. obs: 11119 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 37
Reflection shellResolution: 2→2.05 Å / Redundancy: 9 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 7.6 / Num. unique all: 696 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 531 RANDOM
Rwork0.218 --
all0.229 10853 -
obs-10849 -
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 23 126 1399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.304 34 -
Rwork0.3 --
obs-696 99.4 %

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