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- PDB-3sc0: Crystal Structure of MMACHC (1-238), a human B12 processing enzym... -

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Basic information

Entry
Database: PDB / ID: 3sc0
TitleCrystal Structure of MMACHC (1-238), a human B12 processing enzyme, complexed with MethylCobalamin
ComponentsMethylmalonic aciduria and homocystinuria type C protein
KeywordsOXIDOREDUCTASE / MMACHC / CblC / Cobalamin / Flavin / Glutathione / Flavin Reductase / Maturase
Function / homology
Function and homology information


cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / cobalamin metabolic process / Cobalamin (Cbl) metabolism / demethylation / demethylase activity / glutathione binding ...cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / cobalamin metabolic process / Cobalamin (Cbl) metabolism / demethylation / demethylase activity / glutathione binding / cobalamin binding / FAD binding / glutathione metabolic process / transferase activity / oxidoreductase activity / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Methylmalonic aciduria and homocystinuria type C family / Methylmalonic aciduria and homocystinuria type C family
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / Cyanocobalamin reductase / alkylcobalamin dealkylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKoutmos, M. / Gherasim, C. / Smith, J.L. / Banerjee, R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis of multifunctionality in a vitamin B12-processing enzyme.
Authors: Koutmos, M. / Gherasim, C. / Smith, J.L. / Banerjee, R.
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Apr 25, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.6Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8342
Polymers27,4901
Non-polymers1,3441
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules

A: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6684
Polymers54,9792
Non-polymers2,6892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.955, 105.955, 84.253
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Methylmalonic aciduria and homocystinuria type C protein


Mass: 27489.512 Da / Num. of mol.: 1 / Fragment: B12 binding domain, Residues 1-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMACHC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y4U1
#2: Chemical ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H91CoN13O14P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 2.0 M ammonium sulfate, and 0.1 M Tris.HCl pH 8.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03299 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2010
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03299 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 22523 / Num. obs: 22478 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Χ2: 0.863 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.70.67221621.119198.5
1.97-2.054.80.48221991.1011100
2.05-2.146.90.33122051.0951100
2.14-2.257.60.24722121.0511100
2.25-2.397.70.1922150.9721100
2.39-2.587.70.14122380.8911100
2.58-2.847.70.11422490.8831100
2.84-3.257.60.08322620.7641100
3.25-4.097.50.06423000.6111100
4.09-507.10.04924360.436199.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-IceEpicsdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBY

3sby


Resolution: 1.95→40.293 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.25 / σ(F): 0.14 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1018 5.08 %Random
Rwork0.1862 ---
all0.207 22535 --
obs0.1889 20022 95.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.893 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 90.72 Å2 / Biso mean: 34.0483 Å2 / Biso min: 13.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.9664 Å2-0 Å20 Å2
2---1.9664 Å20 Å2
3---3.9329 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 92 179 2186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.552
X-RAY DIFFRACTIONf_dihedral_angle_d27.904
X-RAY DIFFRACTIONf_chiral_restr0.123
X-RAY DIFFRACTIONf_plane_restr0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
1.95-2.05280.25351370.1962X-RAY DIFFRACTION89
2.0528-2.18140.23861540.1737X-RAY DIFFRACTION93
2.1814-2.34990.23521580.1791X-RAY DIFFRACTION95
2.3499-2.58630.24561520.1729X-RAY DIFFRACTION97
2.5863-2.96040.27431610.188X-RAY DIFFRACTION98
2.9604-3.72940.23551130.1705X-RAY DIFFRACTION99
3.7294-40.30160.22391430.1955X-RAY DIFFRACTION99

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