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- PDB-5nrp: Beta domain of human transcobalamin bound to cobinamide -

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Basic information

Entry
Database: PDB / ID: 5nrp
TitleBeta domain of human transcobalamin bound to cobinamide
ComponentsTranscobalamin-2
KeywordsTRANSPORT PROTEIN / binding protein / bloodstream / alternative substrate / substrate bound
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
COB(II)INAMIDE / CYANIDE ION / Transcobalamin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.569 Å
AuthorsBloch, J.S. / Locher, K.P.
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 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy
Revision 2.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.2May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcobalamin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9764
Polymers11,9701
Non-polymers2,0063
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-1 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.859, 59.859, 70.114
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-621-

HOH

21A-661-

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-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H72CoN11O8
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 0.1 M sodium malonate pH 7.0, 12% 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→41.68 Å / Num. obs: 19877 / % possible obs: 95.53 % / Redundancy: 10.2 % / Net I/σ(I): 16.79

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.569→41.683 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1885 5.01 %
Rwork0.1786 --
obs0.1802 37636 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.569→41.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 138 81 1051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0831028
X-RAY DIFFRACTIONf_angle_d4.3911447
X-RAY DIFFRACTIONf_dihedral_angle_d25.942380
X-RAY DIFFRACTIONf_chiral_restr0.657155
X-RAY DIFFRACTIONf_plane_restr0.039178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5692-1.61160.44031230.45522439X-RAY DIFFRACTION84
1.6116-1.6590.391430.36342721X-RAY DIFFRACTION96
1.659-1.71260.33421490.32052826X-RAY DIFFRACTION96
1.7126-1.77380.30231450.25952755X-RAY DIFFRACTION97
1.7738-1.84480.22511460.21982792X-RAY DIFFRACTION97
1.8448-1.92880.25161470.19852811X-RAY DIFFRACTION97
1.9288-2.03050.22941440.17822764X-RAY DIFFRACTION97
2.0305-2.15770.25351450.16842741X-RAY DIFFRACTION95
2.1577-2.32430.22091390.16922689X-RAY DIFFRACTION94
2.3243-2.55810.27821550.18052839X-RAY DIFFRACTION99
2.5581-2.92820.24241490.18552822X-RAY DIFFRACTION98
2.9282-3.68890.18261530.16512830X-RAY DIFFRACTION98
3.6889-41.69820.17141470.16032722X-RAY DIFFRACTION95

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