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- PDB-5nsa: Beta domain of human transcobalamin bound to Co-beta-[2-(2,4-difl... -

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Basic information

Entry
Database: PDB / ID: 5nsa
TitleBeta domain of human transcobalamin bound to Co-beta-[2-(2,4-difluorophenyl)ethinyl]cobalamin
ComponentsTranscobalamin-2
KeywordsTRANSPORT PROTEIN / binding protein / bloodstream / antivitamin B12
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
Domain of unknown function DUF4430 / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / 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
1-ethynyl-2,4-difluorobenzene / COBALAMIN / Transcobalamin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.273 Å
AuthorsBloch, J.S. / Ruetz, M. / Krautler, B. / 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 25, 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

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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)13,4784
Polymers11,9701
Non-polymers1,5093
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-17 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.721, 62.298, 33.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-679-

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-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-8FS / 1-ethynyl-2,4-difluorobenzene


Mass: 138.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4F2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 0.3 M potassium formate, 17% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→43.85 Å / Num. obs: 33543 / % possible obs: 96.19 % / Redundancy: 6.3 % / Net I/σ(I): 24.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.273→43.846 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1788 3112 4.98 %
Rwork0.1442 --
obs0.1459 62434 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.273→43.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 102 236 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161028
X-RAY DIFFRACTIONf_angle_d2.2841439
X-RAY DIFFRACTIONf_dihedral_angle_d20.713396
X-RAY DIFFRACTIONf_chiral_restr0.629160
X-RAY DIFFRACTIONf_plane_restr0.009184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2733-1.29320.4031950.39931767X-RAY DIFFRACTION61
1.2932-1.31440.5625940.54541828X-RAY DIFFRACTION65
1.3144-1.33710.27471500.24282824X-RAY DIFFRACTION99
1.3371-1.36140.25991500.22322814X-RAY DIFFRACTION99
1.3614-1.38760.26051450.22422841X-RAY DIFFRACTION99
1.3876-1.41590.24281510.19852843X-RAY DIFFRACTION99
1.4159-1.44670.22051470.19972782X-RAY DIFFRACTION99
1.4467-1.48030.23371450.21282777X-RAY DIFFRACTION98
1.4803-1.51730.20941490.14662835X-RAY DIFFRACTION100
1.5173-1.55840.16071540.13062831X-RAY DIFFRACTION100
1.5584-1.60420.17871470.12622856X-RAY DIFFRACTION100
1.6042-1.6560.15451470.11852816X-RAY DIFFRACTION100
1.656-1.71520.17121490.11342846X-RAY DIFFRACTION100
1.7152-1.78390.1311560.11182824X-RAY DIFFRACTION100
1.7839-1.86510.15081470.11232857X-RAY DIFFRACTION100
1.8651-1.96340.25251210.18122454X-RAY DIFFRACTION86
1.9634-2.08640.13221490.11822836X-RAY DIFFRACTION99
2.0864-2.24750.17321380.13242641X-RAY DIFFRACTION93
2.2475-2.47360.14961380.12492695X-RAY DIFFRACTION95
2.4736-2.83150.1431410.12472821X-RAY DIFFRACTION98
2.8315-3.56720.16771490.12652753X-RAY DIFFRACTION98
3.5672-43.87190.1821500.14292781X-RAY DIFFRACTION98

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