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- PDB-6x8z: Crystal structure of N-truncated human B12 chaperone CblD(C262S)-... -

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Basic information

Entry
Database: PDB / ID: 6x8z
TitleCrystal structure of N-truncated human B12 chaperone CblD(C262S)-thiolato-cob(III)alamin complex (108-296)
ComponentsMethylmalonic aciduria and homocystinuria type D protein, mitochondrial
KeywordsOXIDOREDUCTASE / cobalamin / vitamin B12 / chaperone
Function / homology
Function and homology information


Defective MMADHC causes MMAHCD / cobalamin metabolic process / Cobalamin (Cbl) metabolism / mitochondrion / cytoplasm / cytosol
Similarity search - Function
Methylmalonic aciduria and homocystinuria type D protein / Methylmalonic aciduria and homocystinuria type D protein
Similarity search - Domain/homology
COBALAMIN / Cobalamin trafficking protein CblD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMascarenhas, R. / Li, Z. / Koutmos, M. / Banerjee, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1-DK045776 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: An Interprotein Co-S Coordination Complex in the B 12 -Trafficking Pathway.
Authors: Li, Z. / Mascarenhas, R. / Twahir, U.T. / Kallon, A. / Deb, A. / Yaw, M. / Penner-Hahn, J. / Koutmos, M. / Warncke, K. / Banerjee, R.
History
DepositionJun 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3104
Polymers43,6492
Non-polymers2,6612
Water25214
1
A: Methylmalonic aciduria and homocystinuria type D protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1552
Polymers21,8241
Non-polymers1,3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylmalonic aciduria and homocystinuria type D protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1552
Polymers21,8241
Non-polymers1,3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.222, 69.776, 64.266
Angle α, β, γ (deg.)90.000, 101.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 21824.441 Da / Num. of mol.: 2 / Fragment: UNP residues 108-296 / Mutation: C262S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMADHC, C2orf25, CL25022, HSPC161, My011 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3L0, Oxidoreductases
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG8000, 100 mM Tris-HCl, pH 8.5, 200 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→50.637 Å / Num. obs: 15518 / % possible obs: 99.4 % / Redundancy: 4.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 1.213 / Num. unique obs: 1736 / CC1/2: 0.593

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5CV0

5cv0


Resolution: 2.5→50.637 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2787 814 5.26 %
Rwork0.2493 14658 -
obs0.2509 15472 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.93 Å2 / Biso mean: 64.5675 Å2 / Biso min: 30.6 Å2
Refinement stepCycle: final / Resolution: 2.5→50.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 320 14 2722
Biso mean--90.42 49.96 -
Num. residues----308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.65670.38591370.31232411
2.6567-2.86180.37271150.31522434
2.8618-3.14970.31431420.30142432
3.1497-3.60540.30871330.25292432
3.6054-4.5420.23411510.22892457
4.542-50.6370.25621360.22262492

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