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- PDB-5a4r: Crystal structure of a vitamin B12 trafficking protein -

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Basic information

Entry
Database: PDB / ID: 5a4r
TitleCrystal structure of a vitamin B12 trafficking protein
ComponentsMETHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, MITOCHONDRIAL
KeywordsTRANSPORT PROTEIN
Function / homologyCobalamin (Cbl) metabolism / Methylmalonic aciduria and homocystinuria type D protein / Methylmalonic aciduria and homocystinuria type D protein / cobalamin metabolic process / mitochondrion / cytosol / cytoplasm / Cobalamin trafficking protein CblD
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKopec, J. / Fitzpatrick, F. / Froese, D.S. / Velupillai, S. / Nowak, R. / Chalk, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. ...Kopec, J. / Fitzpatrick, F. / Froese, D.S. / Velupillai, S. / Nowak, R. / Chalk, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Fowler, B. / Baumgartner, M.R. / Yue, W.W.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Insights Into the Mmachc-Mmadhc Protein Complex Involved in Vitamin B12 Trafficking.
Authors: Froese, D.S. / Kopec, J. / Fitzpatrick, F. / Schuller, M. / Mccorvie, T.J. / Chalk, R. / Plessl, T. / Fettelschoss, V. / Fowler, B. / Baumgartner, M.R. / Yue, W.W.
History
DepositionJun 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)19,2161
Polymers19,2161
Non-polymers00
Water46826
1
A: METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, MITOCHONDRIAL

A: METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, MITOCHONDRIAL


Theoretical massNumber of molelcules
Total (without water)38,4312
Polymers38,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area2220 Å2
ΔGint-22.4 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.210, 89.530, 64.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, MITOCHONDRIAL / MMADHC


Mass: 19215.596 Da / Num. of mol.: 1 / Fragment: RESIDUES 129-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q99LS1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.8 Å3/Da / Density % sol: 56.06 % / Description: NONE
Crystal growDetails: 22% POLYACRYLIC ACID 5100, 0.02M MAGNESIUM CHLORIDE, 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97826
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97826 Å / Relative weight: 1
ReflectionResolution: 2.25→44.76 Å / Num. obs: 10530 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 55.59 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 31.6
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.765 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 31.53 / Stereochemistry target values: ML
Details: MISSING ELECTRON DENSITY FOR RESIDUES 129 TO 131, 160 TO 168, 237 TO 245
RfactorNum. reflection% reflection
Rfree0.2554 529 5 %
Rwork0.2286 --
obs0.23 10518 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 66.2 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 0 26 1144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071136
X-RAY DIFFRACTIONf_angle_d0.9691539
X-RAY DIFFRACTIONf_dihedral_angle_d14.461395
X-RAY DIFFRACTIONf_chiral_restr0.037181
X-RAY DIFFRACTIONf_plane_restr0.005196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.47650.32541350.26362442X-RAY DIFFRACTION100
2.4765-2.83480.29561230.26122471X-RAY DIFFRACTION100
2.8348-3.57130.28731250.25482494X-RAY DIFFRACTION100
3.5713-44.77380.23031460.20882582X-RAY DIFFRACTION100

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