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- PDB-3sbz: Crystal Structure of Apo-MMACHC (1-244), a human B12 processing enzyme -

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Basic information

Entry
Database: PDB / ID: 3sbz
TitleCrystal Structure of Apo-MMACHC (1-244), a human B12 processing enzyme
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 / glutathione metabolic process / FAD binding / 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
MALONATE ION / Cyanocobalamin reductase / alkylcobalamin dealkylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.4Sep 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)29,3135
Polymers28,9151
Non-polymers3984
Water2,558142
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)58,62710
Polymers57,8302
Non-polymers7968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/31
Buried area4730 Å2
ΔGint-12 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.448, 112.448, 112.136
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

21A-367-

HOH

31A-379-

HOH

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Components

#1: Protein Methylmalonic aciduria and homocystinuria type C protein


Mass: 28915.084 Da / Num. of mol.: 1 / Fragment: B12 binding domain, Residues 1-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMACHC / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y4U1
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.54 Å3/Da / Density % sol: 65.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.9 M sodium malonate, 5% Jeffamine 600 pH 7.0, 0.1 M Hepes 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2009
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: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 27814 / Num. obs: 27786 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.52
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2-2.0710.90.50228251100
2.07-2.15110.32428251100
2.15-2.2511.10.25628341100
2.25-2.3711.30.20228491100
2.37-2.5211.30.16728351100
2.52-2.7111.60.11828511100
2.71-2.9911.90.07428841100
2.99-3.4212.10.06829041100
3.42-4.3111.90.0522940199.9
4.31-5011.10.0393108199.3

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Processing

Software
NameVersionClassification
Blu-IceEpicsdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBY

3sby


Resolution: 2→48.691 Å / SU ML: 0.22 / σ(F): 0.11 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1418 5.1 %RANDOM
Rwork0.1889 ---
all0.1909 28855 --
obs0.1909 27786 96.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.796 Å2 / ksol: 0.43 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.1836 Å20 Å20 Å2
2---8.1836 Å20 Å2
3---16.3671 Å2
Refinement stepCycle: LAST / Resolution: 2→48.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 27 142 2054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081979
X-RAY DIFFRACTIONf_angle_d1.1922704
X-RAY DIFFRACTIONf_dihedral_angle_d17.424728
X-RAY DIFFRACTIONf_chiral_restr0.068283
X-RAY DIFFRACTIONf_plane_restr0.006354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.2531440.21382387X-RAY DIFFRACTION90
2.0715-2.15440.23261400.19952480X-RAY DIFFRACTION93
2.1544-2.25250.23571360.18862512X-RAY DIFFRACTION94
2.2525-2.37120.1981550.18762562X-RAY DIFFRACTION95
2.3712-2.51980.22651510.19322592X-RAY DIFFRACTION97
2.5198-2.71430.26861220.19162663X-RAY DIFFRACTION98
2.7143-2.98740.25341370.20312706X-RAY DIFFRACTION99
2.9874-3.41960.24421640.19082721X-RAY DIFFRACTION100
3.4196-4.3080.19531320.16222793X-RAY DIFFRACTION99
4.308-48.70580.21761370.18792952X-RAY DIFFRACTION99

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