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- PDB-6h9f: Structure of glutamate mutase reconstituted with bishomo-coenzyme B12 -

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Basic information

Entry
Database: PDB / ID: 6h9f
TitleStructure of glutamate mutase reconstituted with bishomo-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 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
Chem-8ZB / COBALAMIN / 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: 2.1 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)140,41010
Polymers136,8904
Non-polymers3,5196
Water24,3921354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-71 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.749, 112.286, 108.010
Angle α, β, γ (deg.)90.000, 95.712, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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 , 4 types, 1360 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-8ZB / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol


Mass: 279.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N5O3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1354 / 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: 0.908 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.1→35.4 Å / Num. obs: 88205 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.74 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.1228 / Rrim(I) all: 0.241 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6425 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 33437 / CC1/2: 0.679 / Rpim(I) all: 0.3826 / Rrim(I) all: 0.7488 / % possible all: 99.8

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Processing

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

1ccw


Resolution: 2.1→35.35 Å / SU ML: 0.2226 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1106
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 4528 5.14 %random selection
Rwork0.1575 ---
obs0.1599 88134 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9604 0 242 1354 11200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006710044
X-RAY DIFFRACTIONf_angle_d0.867713622
X-RAY DIFFRACTIONf_chiral_restr0.04971494
X-RAY DIFFRACTIONf_plane_restr0.00531760
X-RAY DIFFRACTIONf_dihedral_angle_d10.93515910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32141450.24172825X-RAY DIFFRACTION99.83
2.12-2.150.28661500.22242724X-RAY DIFFRACTION99.79
2.15-2.170.25761430.2192790X-RAY DIFFRACTION99.9
2.17-2.20.261370.21512817X-RAY DIFFRACTION99.86
2.2-2.230.30181200.2112749X-RAY DIFFRACTION99.83
2.23-2.260.27311490.20242834X-RAY DIFFRACTION99.9
2.26-2.290.27011430.19712779X-RAY DIFFRACTION99.93
2.29-2.330.25481440.1952746X-RAY DIFFRACTION99.9
2.33-2.370.22951480.19532807X-RAY DIFFRACTION99.9
2.37-2.40.24471450.19192759X-RAY DIFFRACTION99.86
2.4-2.450.22861400.1842810X-RAY DIFFRACTION99.93
2.45-2.490.22791350.17572773X-RAY DIFFRACTION99.97
2.49-2.540.24851520.17042793X-RAY DIFFRACTION99.9
2.54-2.590.21351710.17162734X-RAY DIFFRACTION99.93
2.59-2.650.19711750.16292788X-RAY DIFFRACTION99.97
2.65-2.710.2321260.16262781X-RAY DIFFRACTION100
2.71-2.770.20251510.16072814X-RAY DIFFRACTION99.9
2.77-2.850.21971530.15312741X-RAY DIFFRACTION99.93
2.85-2.930.19731540.14852831X-RAY DIFFRACTION99.93
2.93-3.030.22011680.15412742X-RAY DIFFRACTION99.9
3.03-3.140.1951450.14642789X-RAY DIFFRACTION100
3.14-3.260.19921770.14682758X-RAY DIFFRACTION100
3.26-3.410.19631360.14182804X-RAY DIFFRACTION99.97
3.41-3.590.1591330.13052806X-RAY DIFFRACTION99.97
3.59-3.810.15631520.12082803X-RAY DIFFRACTION100
3.81-4.110.16451460.11262805X-RAY DIFFRACTION99.97
4.11-4.520.13811680.10362793X-RAY DIFFRACTION100
4.52-5.170.131510.10912810X-RAY DIFFRACTION100
5.17-6.510.16241620.14172811X-RAY DIFFRACTION100
6.51-35.350.16662090.14442790X-RAY DIFFRACTION99.4

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