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- PDB-5cuz: Crystal structure of SeMet-substituted N-terminal truncated human... -

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Basic information

Entry
Database: PDB / ID: 5cuz
TitleCrystal structure of SeMet-substituted N-terminal truncated human B12-chaperone CblD (108-296)
ComponentsMethylmalonic aciduria and homocystinuria type D protein, mitochondrial
KeywordsCHAPERONE / 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 metabolic process / Cobalamin (Cbl) metabolism / mitochondrion / cytosol / cytoplasm / Cobalamin trafficking protein CblD
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 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 25, 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

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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


Theoretical massNumber of molelcules
Total (without water)22,0751
Polymers22,0751
Non-polymers00
Water37821
1
A: Methylmalonic aciduria and homocystinuria type D protein, mitochondrial

A: Methylmalonic aciduria and homocystinuria type D protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)44,1502
Polymers44,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2560 Å2
ΔGint-20 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.341, 66.226, 71.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 22074.982 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.8 Å3/Da / Density % sol: 32.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % PEG3350, 0.1M Tris-HCl, pH 7.5, 0.185 M MgCl2, 0.12 M NaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979475 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2013
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: 0.979475 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 6667 / % possible obs: 94.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.5
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.5 / % possible all: 70.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→48.71 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.472 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26266 320 4.8 %RANDOM
Rwork0.20831 ---
obs0.21101 6338 93.83 %-
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: 45.151 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å20 Å2
2--2.45 Å20 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.31→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 0 21 1287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191294
X-RAY DIFFRACTIONr_bond_other_d0.0010.021239
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9561750
X-RAY DIFFRACTIONr_angle_other_deg0.7613.0042816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87524.09861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89815215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.406157
X-RAY DIFFRACTIONr_chiral_restr0.080.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
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: 2.31→2.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 14 -
Rwork0.242 324 -
obs--65.13 %

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