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- PDB-3req: METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRU... -

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Basic information

Entry
Database: PDB / ID: 3req
TitleMETHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)
Components(METHYLMALONYL-COA MUTASE) x 2
KeywordsCOMPLEX (ISOMERASE/DEOXYADENOSINE) / COMPLEX (ISOMERASE-DEOXYADENOSINE) / ISOMERASE / MUTASE / INTRAMOLECULAR TRANSFERASE / COMPLEX (ISOMERASE-DEOXYADENOSINE) complex
Function / homology
Function and homology information


lactate fermentation to propionate and acetate / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / cobalamin binding / metal ion binding / cytoplasm
Similarity search - Function
Methylmalonyl-CoA mutase small subunit, N-terminal / Methylmalonyl-CoA mutase, beta chain / Methylmalonyl-CoA mutase signature. / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin (vitamin B12)-dependent enzyme, catalytic / Cobalamin-binding domain ...Methylmalonyl-CoA mutase small subunit, N-terminal / Methylmalonyl-CoA mutase, beta chain / Methylmalonyl-CoA mutase signature. / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / COBALAMIN / Methylmalonyl-CoA mutase small subunit / Methylmalonyl-CoA mutase large subunit
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEvans, P.R. / Mancia, F.
Citation
Journal: Structure / Year: 1998
Title: Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism.
Authors: Mancia, F. / Evans, P.R.
#1: Journal: Structure / Year: 1996
Title: How Coenzyme B12 Radicals are Generated: The Crystal Structure of Methylmalonyl-Coenzyme a Mutase at 2 A Resolution
Authors: Mancia, F. / Keep, N.H. / Nakagawa, A. / Leadlay, P.F. / Mcsweeney, S. / Rasmussen, B. / Bosecke, P. / Diat, O. / Evans, P.R.
History
DepositionDec 4, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: 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: METHYLMALONYL-COA MUTASE
B: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,1664
Polymers149,5682
Non-polymers1,5982
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-65 kcal/mol
Surface area48250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.910, 110.910, 257.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE CRYSTAL ASYMMETRIC UNIT CONSISTS OF TWO HETERODIMERIC MOLECULES, EACH WITH AN ACTIVE ALPHA CHAIN (CHAINS A AND C), AND AN INACTIVE BETA CHAIN (CHAINS B AND D). EACH ALPHA CHAIN CONTAINS A COBALAMIN, MODELED AS A FIVE-COORDINATE CO (II) SPECIES, AND A COENZYME A MOLECULE APPROXIMATELY IN THE SUBSTRATE BINDING SITE, BUT WITH THE PANTOTHEINE SIDE CHAIN DISORDERED.

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Components

#1: Protein METHYLMALONYL-COA MUTASE


Mass: 80137.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885
Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Gene: MUTA, MUTB / Plasmid: PMEX2 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTA, MUTB / Production host: Escherichia coli (E. coli) / References: UniProt: P11653, methylmalonyl-CoA mutase
#2: Protein METHYLMALONYL-COA MUTASE


Mass: 69430.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885
Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Gene: MUTA, MUTB / Plasmid: PMEX2 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTA, MUTB / Production host: K38 PGP1-2 / References: UniProt: P11652, methylmalonyl-CoA mutase
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
Compound detailsTHIS STRUCTURE IS IN THE OPEN SUBSTRATE-FREE CONFORMATION. THE PROTEIN CONFORMATION IS VERY SIMILAR ...THIS STRUCTURE IS IN THE OPEN SUBSTRATE-FREE CONFORMATION. THE PROTEIN CONFORMATION IS VERY SIMILAR TO THAT IN THE MUCH BETTER DETERMINED NON-PRODUCTIVE COA COMPLEX (2REQ).

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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: 2.6 Å3/Da / Density % sol: 53 %
Description: THE DATA WERE COLLECTED IN 3 PASSES OF DIFFERENT EXPOSURE TIMES BECAUSE OF THE VERY HIGH BFACTOR. THE 3 PASSES MERGED TOGETHER VERY POORLY.
Crystal growMethod: vapor diffusion / pH: 7.5
Details: PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 1MM DTT, TRIS PH 7.5. RESERVOIR: 14% PEG 4000 (W/V), 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL VOLUMES OF PROTEIN SOLUTION ...Details: PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 1MM DTT, TRIS PH 7.5. RESERVOIR: 14% PEG 4000 (W/V), 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL VOLUMES OF PROTEIN SOLUTION AND RESERVOIR MIXED, AND EQUILIBRATED BY VAPOR DIFFUSION., vapor diffusion
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 14 % / Common name: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: 2 MIRRORS, 2 SI(111) CRYSTAL MONOCHROMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29 Å / Num. obs: 44606 / % possible obs: 99.2 % / Observed criterion σ(I): 6 / Redundancy: 9 % / Biso Wilson estimate: 78 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2 / % possible all: 98.7
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2REQ

2req


Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DERIVED FROM ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.393 2224 5 %RANDOM
Rwork0.313 ---
obs-41745 97.6 %-
Displacement parametersBiso mean: 68 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10176 0 109 0 10285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.63
X-RAY DIFFRACTIONp_mcangle_it4.25
X-RAY DIFFRACTIONp_scbond_it4.24
X-RAY DIFFRACTIONp_scangle_it6.16
X-RAY DIFFRACTIONp_plane_restr0.030.03
X-RAY DIFFRACTIONp_chiral_restr0.1560.15
X-RAY DIFFRACTIONp_singtor_nbd0.1280.15
X-RAY DIFFRACTIONp_multtor_nbd0.1660.15
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1330.15
X-RAY DIFFRACTIONp_planar_tor5.315
X-RAY DIFFRACTIONp_staggered_tor2515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3520
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.313
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.85 Å

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