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- PDB-6req: METHYLMALONYL-COA MUTASE, 3-CARBOXYPROPYL-COA INHIBITOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 6req
TitleMETHYLMALONYL-COA MUTASE, 3-CARBOXYPROPYL-COA INHIBITOR COMPLEX
Components(PROTEIN (METHYLMALONYL-COA ...) x 2
KeywordsISOMERASE / MUTASE / INTRAMOLECULAR TRANSFERASE
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
3-CARBOXYPROPYL-COENZYME A / 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: 2.2 Å
AuthorsEvans, P.R. / Mancia, F.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of substrate complexes of methylmalonyl-CoA mutase.
Authors: Mancia, F. / Smith, G.A. / Evans, P.R.
History
DepositionSep 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 9, 1999Provider: 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 1.4Sep 20, 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: PROTEIN (METHYLMALONYL-COA MUTASE)
B: PROTEIN (METHYLMALONYL-COA MUTASE)
C: PROTEIN (METHYLMALONYL-COA MUTASE)
D: PROTEIN (METHYLMALONYL-COA MUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,68810
Polymers299,1364
Non-polymers4,5526
Water20,7171150
1
A: PROTEIN (METHYLMALONYL-COA MUTASE)
B: PROTEIN (METHYLMALONYL-COA MUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8445
Polymers149,5682
Non-polymers2,2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-74 kcal/mol
Surface area46020 Å2
MethodPISA
2
C: PROTEIN (METHYLMALONYL-COA MUTASE)
D: PROTEIN (METHYLMALONYL-COA MUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8445
Polymers149,5682
Non-polymers2,2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-75 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.950, 160.460, 88.480
Angle α, β, γ (deg.)90.00, 105.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.462535, -0.028377, 0.886147), (0.022663, -0.999539, -0.020179), (0.886311, 0.01075, 0.462965)
Vector: 14.295, 161.11501, -7.701)
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS TWO HETERODIMERIC MOLECULES, EACH WITH AN ALPHA CHAIN (CHAINS A AND C, CORRESPONDING TO GENE MUTB) AND A BETA CHAIN (CHAINS B AND D, CORRESPONDING TO GENE MUTA). MOLECULE 1 CONSISTS OF CHAINS A (ALPHA), B (BETA), WITH GLYCEROL (RESIDUE 3001) AND WATERS (1-580). MOLECULE 2 CONSISTS OF CHAINS C (ALPHA), D (BETA), WITH GLYCEROL (RESIDUE 3002) AND WATERS (581-1155). CHAIN A INCLUDES COENZYME B12 (RESIDUE 1800) AND THE INHIBITOR 3-CARBOXYPROPYL-COA (RESIDUE 1801). CHAIN C INCLUDES COENZYME B12 (RESIDUE 2800) AND THE INHIBITOR 3-CARBOXYPROPYL-COA (RESIDUE 2801).

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Components

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PROTEIN (METHYLMALONYL-COA ... , 2 types, 4 molecules ACBD

#1: Protein PROTEIN (METHYLMALONYL-COA MUTASE)


Mass: 80137.852 Da / Num. of mol.: 2 / Fragment: ALPHA-SUBUNIT
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 ARE COEXPRESSED FROM THE SAME PLASMID;
Gene: MUTB / Plasmid: PMEX1 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTB / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: P11653, methylmalonyl-CoA mutase
#2: Protein PROTEIN (METHYLMALONYL-COA MUTASE)


Mass: 69430.188 Da / Num. of mol.: 2 / Fragment: BETA-SUBUNIT
Source method: isolated from a genetically manipulated source
Details: ALPHA CHAINS A AND C INCLUDE COENZYME B12, AND THE INHIBITOR 3-CARBOXYPROPYL- COENZYME A . B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R.
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885
Description: THE 2 GENES ARE COEXPRESSED FROM THE SAME PLASMID
Gene: MUTA / Plasmid: PMEX1 / Cellular location (production host): CYTOPLASM / Gene (production host): MUTA / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: P11652, methylmalonyl-CoA mutase

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Non-polymers , 4 types, 1156 molecules

#3: Chemical ChemComp-3CP / 3-CARBOXYPROPYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O18P3S
#4: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / 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: 2.74 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
21 mMAdoCbl1drop
31 mMdithiothreitol1drop
42-10 mMsuccinyl-CoA1dropor 2- or 3-carboxypropyl-CoA
5100 mMTris-HCl1drop
617-18 %PEG40001reservoir
7100 mMTris-HCl1reservoir
80.01 %1reservoirNaN3
920 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.24
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRROR
RadiationMonochromator: DOUBLE SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.16→99 Å / Num. obs: 170993 / % possible obs: 98 % / Observed criterion σ(I): 6 / Redundancy: 3.3 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.1
Reflection shellResolution: 2.16→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.261 / % possible all: 87.2
Reflection
*PLUS
Highest resolution: 2.16 Å / Lowest resolution: 16 Å / Num. obs: 161729 / % possible obs: 98.9 % / Observed criterion σ(I): 6 / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Biso Wilson estimate: 36 Å2
Reflection shell
*PLUS
% possible obs: 98.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 8.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1REQ

1req


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.23 / Details: NCS RESTRAINTS BETWEEN TWO MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.263 7413 4.6 %SAME AS 1REQ
Rwork0.206 ---
obs0.216 161381 98.9 %-
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20.82 Å2
2---0.4 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20664 0 302 1150 22116
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.93
X-RAY DIFFRACTIONp_mcangle_it3.85
X-RAY DIFFRACTIONp_scbond_it4.34
X-RAY DIFFRACTIONp_scangle_it5.66
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd0.1370.15
X-RAY DIFFRACTIONp_multtor_nbd0.1890.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.15
X-RAY DIFFRACTIONp_xyhbond_nbd0.1320.15
X-RAY DIFFRACTIONp_planar_tor2.87
X-RAY DIFFRACTIONp_staggered_tor17.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.820
X-RAY DIFFRACTIONp_special_tor

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