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- PDB-6h9e: Structure of glutamate mutase reconstituted with homo-coenzyme B12 -

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Basic information

Entry
Database: PDB / ID: 6h9e
TitleStructure of glutamate mutase reconstituted with homo-coenzyme B12
Components(Glutamate mutase ...) x 2
KeywordsISOMERASE / COENZYME B12 / CO-C-BOND / 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
COBALAMIN / Chem-FWK / 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: 1.82 Å
AuthorsGruber, K. / Csitkovits, V. / Kratky, C.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues.
Authors: Gruber, K. / Csitkovits, V. / Lyskowski, A. / Kratky, C. / Krautler, B.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate mutase sigma subunit
B: Glutamate mutase epsilon subunit
C: Glutamate mutase sigma subunit
D: Glutamate mutase epsilon subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,84215
Polymers136,8904
Non-polymers3,95211
Water26,5181472
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15050 Å2
ΔGint-74 kcal/mol
Surface area40430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.890, 112.620, 108.350
Angle α, β, γ (deg.)90.000, 95.690, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Glutamate mutase ... , 2 types, 4 molecules ACBD

#1: Protein Glutamate mutase sigma subunit / Glutamate mutase S chain / Glutamate mutase small subunit / Methylaspartate mutase


Mass: 14830.991 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: small subunit / Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: glmS / Production host: Escherichia coli (E. coli) / References: UniProt: P80078, methylaspartate mutase
#2: Protein Glutamate mutase epsilon subunit / Glutamate mutase E chain / Glutamate mutase large subunit / Methylaspartate mutase


Mass: 53614.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: large subunit / Source: (gene. exp.) Clostridium cochlearium (bacteria) / Gene: glmE / Production host: Escherichia coli (E. coli) / References: UniProt: P80077, methylaspartate mutase

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Non-polymers , 5 types, 1483 molecules

#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FWK / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol


Mass: 265.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1472 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 6% (w/v) PEG-4000, 0.1 M DL-tartrate, pH=4.5, 2 mM CdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8428 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8428 Å / Relative weight: 1
ReflectionResolution: 1.82→40.41 Å / Num. obs: 130639 / % possible obs: 96.1 % / Redundancy: 3 % / Biso Wilson estimate: 13.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0525 / Rpim(I) all: 0.0352 / Rrim(I) all: 0.0635 / Net I/σ(I): 19.5
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.2994 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 12636 / CC1/2: 0.915 / Rpim(I) all: 0.2071 / Rrim(I) all: 0.3658 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ccw

1ccw


Resolution: 1.82→40.41 Å / SU ML: 0.1594 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1663
RfactorNum. reflection% reflectionSelection details
Rfree0.1675 6647 5.09 %random selection
Rwork0.1368 ---
obs0.1384 130627 96.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.92 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9604 0 270 1472 11346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006610227
X-RAY DIFFRACTIONf_angle_d0.843613893
X-RAY DIFFRACTIONf_chiral_restr0.05211521
X-RAY DIFFRACTIONf_plane_restr0.00571797
X-RAY DIFFRACTIONf_dihedral_angle_d9.86746087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.33552090.27563517X-RAY DIFFRACTION83.49
1.84-1.860.20152010.16834231X-RAY DIFFRACTION98.1
1.86-1.890.2061850.16924223X-RAY DIFFRACTION97.89
1.89-1.910.22432290.18014237X-RAY DIFFRACTION97.98
1.91-1.940.23882200.20044226X-RAY DIFFRACTION97.61
1.94-1.960.2112250.15594149X-RAY DIFFRACTION97.85
1.96-1.990.20092110.15354206X-RAY DIFFRACTION97.89
1.99-2.020.20342100.14834180X-RAY DIFFRACTION97.4
2.02-2.050.19442360.14644202X-RAY DIFFRACTION97.73
2.05-2.090.16832300.14084208X-RAY DIFFRACTION97.58
2.09-2.120.18062350.12754145X-RAY DIFFRACTION97.27
2.12-2.160.15352070.12774190X-RAY DIFFRACTION97.62
2.16-2.20.17292320.13374185X-RAY DIFFRACTION97.55
2.2-2.250.18262250.16074151X-RAY DIFFRACTION97.14
2.25-2.30.22212030.15884205X-RAY DIFFRACTION96.96
2.3-2.350.17182430.13664144X-RAY DIFFRACTION97.19
2.35-2.410.17372300.13624145X-RAY DIFFRACTION96.77
2.41-2.470.16852010.13164195X-RAY DIFFRACTION97
2.47-2.550.19452490.13254132X-RAY DIFFRACTION96.6
2.55-2.630.16222310.13344124X-RAY DIFFRACTION96.46
2.63-2.720.15712420.12714089X-RAY DIFFRACTION96.27
2.72-2.830.16082350.12964143X-RAY DIFFRACTION96.07
2.83-2.960.16232620.12574078X-RAY DIFFRACTION95.89
2.96-3.110.14822350.12464125X-RAY DIFFRACTION95.82
3.11-3.310.16312090.13174139X-RAY DIFFRACTION95.46
3.31-3.570.1432150.12454120X-RAY DIFFRACTION95.34
3.57-3.920.142360.11844078X-RAY DIFFRACTION94.65
3.92-4.490.11211800.1084114X-RAY DIFFRACTION94.08
4.49-5.660.13672190.12184052X-RAY DIFFRACTION93.58
5.66-40.420.15312020.1434047X-RAY DIFFRACTION91.34

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