- PDB-5a4r: Crystal structure of a vitamin B12 trafficking protein -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5a4r
Title
Crystal structure of a vitamin B12 trafficking protein
Components
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, MITOCHONDRIAL
Keywords
TRANSPORT PROTEIN
Function / homology
Cobalamin (Cbl, vitamin B12) transport and metabolism / Methylmalonic aciduria and homocystinuria type D protein / Methylmalonic aciduria and homocystinuria type D protein / cobalamin metabolic process / mitochondrion / cytoplasm / Cobalamin trafficking protein CblD
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97826 Å / Relative weight: 1
Reflection
Resolution: 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 shell
Resolution: 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
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Rfree
0.2554
529
5 %
Rwork
0.2286
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obs
0.23
10518
99.77 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parameters
Biso mean: 66.2 Å2
Refinement step
Cycle: LAST / Resolution: 2.25→44.765 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1118
0
0
26
1144
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
1136
X-RAY DIFFRACTION
f_angle_d
0.969
1539
X-RAY DIFFRACTION
f_dihedral_angle_d
14.461
395
X-RAY DIFFRACTION
f_chiral_restr
0.037
181
X-RAY DIFFRACTION
f_plane_restr
0.005
196
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.2501-2.4765
0.3254
135
0.2636
2442
X-RAY DIFFRACTION
100
2.4765-2.8348
0.2956
123
0.2612
2471
X-RAY DIFFRACTION
100
2.8348-3.5713
0.2873
125
0.2548
2494
X-RAY DIFFRACTION
100
3.5713-44.7738
0.2303
146
0.2088
2582
X-RAY DIFFRACTION
100
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