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- PDB-1i9c: GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENO... -

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Basic information

Entry
Database: PDB / ID: 1i9c
TitleGLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENOSYLCOBALAMIN AND SUBSTRATE
Components(GLUTAMATE MUTASE) x 2
KeywordsISOMERASE / COENZYME B12 / RADICAL REACTION / RIBOSE PSEUDOROTATION / 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
(2S,3S)-3-methyl-aspartic acid / 5'-DEOXYADENOSINE / COBALAMIN / GLUTAMIC ACID / Glutamate mutase epsilon subunit / Glutamate mutase sigma subunit
Similarity search - Component
Biological speciesClostridium cochlearium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.9 Å
AuthorsGruber, K. / Kratky, C.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2001
Title: Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase
Authors: Gruber, K. / Reitzer, R. / Kratky, C.
#1: Journal: Structure / Year: 1999
Title: Glutamate Mutase from Clostridum 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.
#2: 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.
#3: Journal: Eur.J.Biochem. / Year: 1994
Title: Characterization of the Coenzyme-B12-Dependent Glutamate Mutase from Clostridium Cochlearium Produced in Escherischia Coli
Authors: Zelder, O. / Beatrix, B. / Leutbecher, U. / Buckel, W.
History
DepositionMar 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.5Aug 9, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE MUTASE
B: GLUTAMATE MUTASE
C: GLUTAMATE MUTASE
D: GLUTAMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,66012
Polymers136,9084
Non-polymers3,7528
Water22,6631258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-39 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.348, 113.139, 108.439
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the heterotetramer present in the asymmetric unit

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein GLUTAMATE MUTASE / METHYLASPARTATE MUTASE SMALL CHAIN


Mass: 14830.991 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: GLMS / Plasmid: POZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: P80078, methylaspartate mutase
#2: Protein GLUTAMATE MUTASE / METHYLASPARTATE MUTASE E CHAIN


Mass: 53623.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ADENOSYLCOBALAMAIN AND A MIXTURE OF GLUTAMATE AND 2S,3S-3-METHYLASPARTIC ACID
Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: GLME / Plasmid: POZ5 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P80077, methylaspartate mutase

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Non-polymers , 5 types, 1266 molecules

#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#5: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Chemical ChemComp-2AS / (2S,3S)-3-methyl-aspartic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Comment: antibiotic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1258 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG-4000, cadmium chloride, coenzyme B12, sodium glutamate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.5 mg/mlprotein1drop
20.5 mg/mlcoenzyme B121drop
32 mM1dropCdCl2
46 %(w/v)PEG40001reservoir
50.1 MNa-S-glutamate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8439
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8439 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 121680 / Num. obs: 121680 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 18.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5 / Num. unique all: 8102 / Rsym value: 0.281 / % possible all: 100
Reflection
*PLUS
Num. measured all: 555148
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 8102 / Num. measured obs: 30037

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Processing

Software
NameClassification
SHELXL-97refinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: 1CCW

1ccw


Resolution: 1.9→30 Å / Num. parameters: 45086 / Num. restraintsaints: 56174 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 0 / σ(I): 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
RfactorNum. reflection% reflectionSelection details
Rfree0.221 6137 5 %RANDOM
Rwork0.168 ---
all0.1705 121680 --
obs0.1705 121680 99.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 13.3 Å2
Refine analyzeNum. disordered residues: 39 / Occupancy sum hydrogen: 9804 / Occupancy sum non hydrogen: 11102
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9606 0 258 1258 11122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0.032
X-RAY DIFFRACTIONs_from_restr_planes0.34
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.34
X-RAY DIFFRACTIONs_chiral_restr0.045

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