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- PDB-5req: Methylmalonyl-COA MUTASE, Y89F Mutant, substrate complex -

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Basic information

Entry
Database: PDB / ID: 5req
TitleMethylmalonyl-COA MUTASE, Y89F Mutant, substrate complex
Components(PROTEIN (METHYLMALONYL-COA MUTASE ...) 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
Regulator of G-protein Signalling 4; domain 1 - #20 / 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 / Regulator of G-protein Signalling 4; domain 1 ...Regulator of G-protein Signalling 4; domain 1 - #20 / 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 / Regulator of G-protein Signalling 4; domain 1 / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / METHYLMALONYL(CARBADETHIA)-COENZYME A / SUCCINYL(CARBADETHIA)-COENZYME A / 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. / Thomae, N.H.
CitationJournal: Biochemistry / Year: 1998
Title: Stabilization of radical intermediates by an active-site tyrosine residue in methylmalonyl-CoA mutase.
Authors: Thoma, N.H. / Meier, T.W. / Evans, P.R. / Leadlay, P.F.
History
DepositionAug 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 12, 1998Provider: 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 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.5Sep 20, 2023Group: 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: PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)
B: PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)
C: PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)
D: PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,53114
Polymers299,1044
Non-polymers6,42710
Water19,7081094
1
A: PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)
B: PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,7667
Polymers149,5522
Non-polymers3,2145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13830 Å2
ΔGint-80 kcal/mol
Surface area45900 Å2
MethodPISA
2
C: PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)
D: PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,7667
Polymers149,5522
Non-polymers3,2145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-81 kcal/mol
Surface area45790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.200, 161.890, 88.700
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.466239, 0.004153, -0.884649), (0.005659, -0.999983, -0.001713), (-0.884641, -0.004207, -0.466255)
Vector: 48.099, 121.602, 42.923)
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 AND WATERS. MOLECULE 2 CONSISTS OF CHAINS C (ALPHA), D (BETA), WITH GLYCEROL AND WATERS. CHAINS A AND C INCLUDE COENZYME B12 (RESIDUE 1800 AND 2800), A 1:1 MIXTURE OF NON-PHYSIOLOGICAL SUBSTRATE AND PRODUCT, SUCCINYL(CARBADETHIA)-COA (RESIDUE 1801 AND 2801) AND METHYLMALONYL(CARBADETHIA)-COA (RESIDUE 1802 AND 2802)

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Components

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

#1: Protein PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)


Mass: 80121.852 Da / Num. of mol.: 2 / Mutation: Y89F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885 / Gene: MUTB / Plasmid: PMEX1-Y89F / Culture collection (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: P11653, methylmalonyl-CoA mutase
#2: Protein PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)


Mass: 69430.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885 / Gene: MUTA / Plasmid: PMEX1-Y89F / Culture collection (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: P11652, methylmalonyl-CoA mutase

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Non-polymers , 5 types, 1104 molecules

#3: Chemical ChemComp-SCD / SUCCINYL(CARBADETHIA)-COENZYME A


Mass: 849.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H42N7O19P3
#4: Chemical ChemComp-MCD / METHYLMALONYL(CARBADETHIA)-COENZYME A


Mass: 849.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H42N7O19P3
#5: Chemical ChemComp-B12 / COBALAMIN


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS ...THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS NO ELECTRON DENSITY FOR AN ADENOSYL GROUP LINKED TO THE COBALT ATOM. RESIDUES 1801 AND 1802 (& 2801, 2802) REPRESENT AN EQUIMOLAR MIXTURE OF SUBSTRATE AND PRODUCT, SUCCINYL (CARBADETHIA)- AND METHYLMALONYL(CARBADETHIA)-COENZYME A.

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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-ID
120 mg/mlprotein1drop
20.100 mMAdoCbl1drop
34 mMsuccinylcarbadethia-CoA1drop
414 %(w/v)PEG40001drop
520 %(v/v)glycerol1drop
6100 mMTris-HCl1drop
714 %(w/v)PEG40001reservoir
820 %(v/v)glycerol1reservoir
9100 mMTris-HCl1reservoir

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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: Nov 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: 45 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: 99 Å / Observed criterion σ(I): 6 / Redundancy: 3.3 % / Biso Wilson estimate: 45 Å2
Reflection shell
*PLUS
Redundancy: 3.5 % / Mean I/σ(I) obs: 5.1

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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: 1REQ

1req


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: NCS RESTRAINTS BETWEEN TWO MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.292 7634 4.6 %SAME AS 1REQ
Rwork0.246 ---
obs0.256 165507 99.9 %-
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å21.27 Å2
2--0.72 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20592 0 426 1094 22112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.63
X-RAY DIFFRACTIONp_mcangle_it2.45
X-RAY DIFFRACTIONp_scbond_it2.44
X-RAY DIFFRACTIONp_scangle_it3.46
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1160.15
X-RAY DIFFRACTIONp_singtor_nbd0.1240.15
X-RAY DIFFRACTIONp_multtor_nbd0.1640.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.15
X-RAY DIFFRACTIONp_xyhbond_nbd0.110.15
X-RAY DIFFRACTIONp_planar_tor5.37
X-RAY DIFFRACTIONp_staggered_tor18.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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