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- PDB-5no0: Beta domain of human transcobalamin in apo form -

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Basic information

Entry
Database: PDB / ID: 5no0
TitleBeta domain of human transcobalamin in apo form
ComponentsTranscobalamin-2
KeywordsTRANSPORT PROTEIN / transcobalamin / apo / substrate-free / TC-beta
Function / homology
Function and homology information


Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / cobalt ion transport / cobalamin transport / cobalamin binding / lysosomal lumen / external side of plasma membrane / extracellular space ...Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / cobalt ion transport / cobalamin transport / cobalamin binding / lysosomal lumen / external side of plasma membrane / extracellular space / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / : / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.57 Å
AuthorsBloch, J.S. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_166672 Switzerland
CitationJournal: PLoS ONE / Year: 2017
Title: Structure of the human transcobalamin beta domain in four distinct states.
Authors: Bloch, J.S. / Ruetz, M. / Krautler, B. / Locher, K.P.
History
DepositionApr 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Transcobalamin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0622
Polymers11,9701
Non-polymers921
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-0 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.979, 59.979, 70.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-636-

HOH

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Components

#1: Protein Transcobalamin-2 / TC-2 / Transcobalamin II / TCII


Mass: 11969.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCN2, TC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20062
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M sodium chloride, 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→41.72 Å / Num. obs: 20772 / % possible obs: 99.76 % / Redundancy: 9.8 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.57→41.723 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 1964 5.01 %
Rwork0.1552 --
obs0.1574 39193 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→41.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 6 143 970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005896
X-RAY DIFFRACTIONf_angle_d0.8361227
X-RAY DIFFRACTIONf_dihedral_angle_d19.673339
X-RAY DIFFRACTIONf_chiral_restr0.053141
X-RAY DIFFRACTIONf_plane_restr0.006159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5704-1.60960.31881350.29782580X-RAY DIFFRACTION97
1.6096-1.65310.34851450.2852662X-RAY DIFFRACTION99
1.6531-1.70180.30711380.26362648X-RAY DIFFRACTION100
1.7018-1.75670.27411390.23992667X-RAY DIFFRACTION100
1.7567-1.81950.25531440.23252695X-RAY DIFFRACTION100
1.8195-1.89240.27421360.1842666X-RAY DIFFRACTION100
1.8924-1.97850.19731350.14462639X-RAY DIFFRACTION100
1.9785-2.08280.17341390.13192675X-RAY DIFFRACTION100
2.0828-2.21330.20531420.13152677X-RAY DIFFRACTION100
2.2133-2.38420.20891400.13392664X-RAY DIFFRACTION100
2.3842-2.6240.22671430.14362675X-RAY DIFFRACTION100
2.624-3.00370.16351460.14742659X-RAY DIFFRACTION100
3.0037-3.78390.15631410.13692677X-RAY DIFFRACTION100
3.7839-41.73740.19911410.15722645X-RAY DIFFRACTION99

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