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- PDB-5cv0: Crystal structure of N-terminal truncated human B12-chaperone Cbl... -

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Basic information

Entry
Database: PDB / ID: 5cv0
TitleCrystal structure of N-terminal truncated human B12-chaperone CblD (108-296)
ComponentsMethylmalonic aciduria and homocystinuria type D protein, mitochondrial
KeywordsOXIDOREDUCTASE / Vitamin B12 / Nitro-FMN-reductase
Function / homologyMethylmalonic aciduria and homocystinuria type D protein / Methylmalonic aciduria and homocystinuria type D protein / Defective MMADHC causes MMAHCD / Cobalamin (Cbl) metabolism / cobalamin metabolic process / mitochondrion / cytosol / cytoplasm / Cobalamin trafficking protein CblD
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYamada, K. / Gherasim, C. / Banerjee, R. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association13SDG14560056 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases.
Authors: Yamada, K. / Gherasim, C. / Banerjee, R. / Koutmos, M.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylmalonic aciduria and homocystinuria type D protein, mitochondrial
B: Methylmalonic aciduria and homocystinuria type D protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)43,6812
Polymers43,6812
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-21 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.638, 67.111, 66.219
Angle α, β, γ (deg.)90.00, 110.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methylmalonic aciduria and homocystinuria type D protein, mitochondrial


Mass: 21840.506 Da / Num. of mol.: 2 / Fragment: UNP residues 108-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMADHC, C2orf25, CL25022, HSPC161, My011 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q9H3L0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % PEG3350, 0.1M Tris-HCl, pH 7.5, 0.2 M MgCl2, 0.1 M NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03299 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2012
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. obs: 30281 / % possible obs: 98.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.5 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5CUZ

5cuz


Resolution: 1.9→31.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.213 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22722 1523 5 %RANDOM
Rwork0.18598 ---
obs0.18811 28735 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.348 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å2-0.78 Å2
2--0.32 Å20 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.9→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 0 303 2958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192725
X-RAY DIFFRACTIONr_bond_other_d0.0010.022526
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9453690
X-RAY DIFFRACTIONr_angle_other_deg0.78135828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89224.552134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46815469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0451514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 95 -
Rwork0.275 1935 -
obs--90.14 %

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