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- PDB-1ccw: STRUCTURE OF THE COENZYME B12 DEPENDENT ENZYME GLUTAMATE MUTASE F... -

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Basic information

Entry
Database: PDB / ID: 1ccw
TitleSTRUCTURE OF THE COENZYME B12 DEPENDENT ENZYME GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM
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 glutamate catabolic process / methylaspartate mutase activity / 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-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / 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-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / 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
CYANOCOBALAMIN / D(-)-TARTARIC ACID / Glutamate mutase epsilon subunit / Glutamate mutase sigma subunit
Similarity search - Component
Biological speciesClostridium cochlearium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsReitzer, R. / Gruber, K. / 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 1, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 1, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 2.0Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 2.1Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)139,9198
Polymers136,9064
Non-polymers3,0134
Water33,2021843
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-72 kcal/mol
Surface area40700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.430, 113.050, 108.300
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.980228, -0.006307, 0.197767), (-0.006522, 0.999978, 0.000439), (0.19776, -0.00172, -0.980249)
Vector: -16.04166, 31.37638, 161.59927)

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Components

#1: Protein PROTEIN (GLUTAMATE MUTASE) / E.C.5.4.99.1 / methylaspartate mutase / component S


Mass: 14830.046 Da / Num. of mol.: 2 / Fragment: B12-Binding Subunit
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): MC4100 / References: UniProt: P80078, methylaspartate mutase
#2: Protein PROTEIN (GLUTAMATE MUTASE) / E.C.5.4.99.1 / METHYLASPARTATE MUTASE / E CHAIN


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


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#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.: 1843 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6 / Details: pH 4.6, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1(2S,3S)-4-FLUOROGLUTAMATE11
2CDCL211
3VITAMIN B1211
4PEG 600011
5D/L TARTARIC ACID11
Crystal grow
*PLUS
pH: 7.5
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: 0.9058
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9058 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 190420 / Num. obs: 190420 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.031 / Rsym value: 0.065 / Net I/σ(I): 5.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.173 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 441525 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.173

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CCP4model building
SHELXL-97refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→30 Å / Num. parameters: 46798 / Num. restraintsaints: 54934 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J. APPL. CRYST. 28 (1995) 53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1728 19177 11.2 %THIN SHELLS
all0.1371 171243 --
obs0.1369 -84.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 9641.9 / Occupancy sum non hydrogen: 11680
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9606 0 206 1843 11655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0.033
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.034
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.136 / Rfactor obs: 0.123 / Rfactor Rfree: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.2
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg23
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.5

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