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- PDB-1cb7: GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM RECONSTITUTED WITH ... -

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Basic information

Entry
Database: PDB / ID: 1cb7
TitleGLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM RECONSTITUTED WITH METHYL-COBALAMIN
Components(PROTEIN (GLUTAMATE MUTASE)) x 2
KeywordsISOMERASE / GLUTAMATE MUTASE / COENZYME-B12 / RADICAL REACTION / TIM-BARREL / ROSSMAN-FOLD
Function / homology
Function and homology information


methylaspartate mutase / anaerobic L-glutamate catabolic process / methylaspartate mutase activity / L-glutamate catabolic process via L-citramalate / cobalamin binding / metal ion binding
Similarity search - Function
Glutamate mutase, C-terminal domain / Glutamate mutase, C-terminal domain - #10 / Glutamate mutase epsilon subunit / Glutamate mutase E subunit, C-terminal domain superfamily / Methylaspartate mutase E chain (MutE) / Glutamate mutase sigma subunit / Methylmalonyl-CoA mutase / Cobalamin (vitamin B12)-dependent enzyme, catalytic / Cobalamin-binding domain / B12 binding domain ...Glutamate mutase, C-terminal domain / Glutamate mutase, C-terminal domain - #10 / Glutamate mutase epsilon subunit / Glutamate mutase E subunit, C-terminal domain superfamily / Methylaspartate mutase E chain (MutE) / Glutamate mutase sigma subunit / Methylmalonyl-CoA mutase / Cobalamin (vitamin B12)-dependent enzyme, catalytic / Cobalamin-binding domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / D(-)-TARTARIC ACID / Glutamate mutase epsilon subunit / Glutamate mutase sigma subunit
Similarity search - Component
Biological speciesClostridium cochlearium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGruber, K. / Reitzer, R. / Kratky, C.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights.
Authors: Reitzer, R. / Gruber, K. / Jogl, G. / Wagner, U.G. / Bothe, H. / Buckel, W. / Kratky, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray analysis of recombinant glutamate mutase and of the isolated component S from Clostridium cochlearium.
Authors: Reitzer, R. / Krasser, M. / Jogl, G. / Buckel, W. / Bothe, H. / Kratky, C.
#2: Journal: Eur.J.Biochem. / Year: 1994
Title: Characterization of the coenzyme-B12-dependent glutamate mutase from Clostridium cochlearium produced in Escherichia coli.
Authors: Zelder, O. / Beatrix, B. / Leutbecher, U. / Buckel, W.
History
DepositionMar 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / diffrn_source / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GLUTAMATE MUTASE)
B: PROTEIN (GLUTAMATE MUTASE)
C: PROTEIN (GLUTAMATE MUTASE)
D: PROTEIN (GLUTAMATE MUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8958
Polymers136,9064
Non-polymers2,9894
Water18,2491013
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13760 Å2
ΔGint-75 kcal/mol
Surface area40780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.330, 113.140, 108.610
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9804, -0.0042, 0.1969), (-0.0046, -1, 0.0013), (0.1969, -0.0022, -0.9804)
Vector: -16.037, 31.1651, 162.12891)

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Components

#1: Protein PROTEIN (GLUTAMATE MUTASE)


Mass: 14830.046 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAINS A, C, B, D FORM HETEROTETRAMER WHICH IS THE BIOLOGICAL UNIT.
Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: GLMS / Plasmid: POZ3 / Gene (production host): GLMS / Production host: Escherichia coli (E. coli) / Strain (production host): MC 4100, DH5 ALPHA / References: UniProt: P80078, methylaspartate mutase
#2: Protein PROTEIN (GLUTAMATE MUTASE)


Mass: 53623.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH CO-METHYLCOBALAMIN / Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: GLME / Plasmid: POZ5 / Gene (production host): GLME / Production host: Escherichia coli (E. coli) / Strain (production host): MC 4100, DH5 ALPHA / References: UniProt: P80077, methylaspartate mutase
#3: Chemical ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H91CoN13O14P
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1013 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growpH: 4.5 / Details: pH 4.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2sodium tartarate11
3METHYL COBALAMIN11
4CdCl211
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 mg/mlprotein1drop
22 mM1dropCdCl2
35 mM(2S,4S)-45-fluoroglutamate1drop
42.5 mg/mlB12(cyano-or-methylcobalamin)1drop
510 mMNa cacodylate1drop
66 %(w/v)PEG40001reservoir
7100 MDL-tartaric acid1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 100016 / % possible obs: 96.1 % / Redundancy: 2.6 % / Rsym value: 0.076 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.189 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 258385 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.189

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Processing

Software
NameVersionClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GLUTAMATE MUTASE RECONSTITUTED WITH CYANOCOBALAMIN

Resolution: 2→25 Å / Num. parameters: 43322 / Num. restraintsaints: 54994 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY APPROX. 0.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 10040 10 %THIN SHELLS
obs0.1597 100016 96.1 %-
all-100016 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-203
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 9832 / Occupancy sum non hydrogen: 10823
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9606 0 204 1013 10823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.029
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.166 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg24
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.3

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