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- PDB-2bbc: Structure of Cobalamin-complexed Bovine Transcobalamin in trigona... -

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Basic information

Entry
Database: PDB / ID: 2bbc
TitleStructure of Cobalamin-complexed Bovine Transcobalamin in trigonal crystal form
ComponentsTranscobalamin IITranscobalamin
KeywordsTRANSPORT PROTEIN / alpha_6 - alpha_6 barrel
Function / homology
Function and homology information


Transport of RCbl within the body / cobalt ion transport / cobalamin transport / cobalamin binding / extracellular space / metal ion binding
Similarity search - Function
Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Cobalamin (vitamin B12)-binding protein / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COBALAMIN / Transcobalamin-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for mammalian vitamin B12 transport by transcobalamin.
Authors: Wuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.6Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcobalamin II
A: COBALAMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7525
Polymers46,3151
Non-polymers1,4374
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.570, 99.570, 128.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 46315.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TCN2, TC2 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD 1168 / References: UniProt: Q9XSC9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% PEG 8000, 0.2M magnesium acetate, 20% 2-methyl-2,4-pentadiol, 0.1M TRIS 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2004
RadiationMonochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 29190 / Num. obs: 29142 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.054 / Χ2: 0.922 / Net I/σ(I): 24.3
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 2875 / Num. unique all: 2875 / Χ2: 1.096 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of Bovine Transcobalamin in monoclinic crystal form (PDB 2BB6).
Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.981 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1192 4.1 %RANDOM
Rwork0.204 ---
all0.205 27934 --
obs0.205 27934 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 94 185 3533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223425
X-RAY DIFFRACTIONr_angle_refined_deg1.5432.0214669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80423.81147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00315600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1751526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022576
X-RAY DIFFRACTIONr_nbd_refined0.2250.21830
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.216
X-RAY DIFFRACTIONr_mcbond_it0.951.52068
X-RAY DIFFRACTIONr_mcangle_it1.76823327
X-RAY DIFFRACTIONr_scbond_it2.23931357
X-RAY DIFFRACTIONr_scangle_it3.594.51342
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 76 -
Rwork0.312 2011 -
all-2087 -
obs--98.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8277-2.6210.84572.99-1.04810.3774-0.09350.2459-0.2514-0.0141-0.10150.15430.1126-0.0330.1950.05650.05370.0262-0.0639-0.03930.00813.137837.857316.5895
20.4581-0.0992-0.03941.40190.44012.226-0.06520.0613-0.06220.1444-0.07390.18120.0269-0.30420.1391-0.06380.05790.0572-0.0398-0.0285-0.04923.821946.795619.1564
348.9529-72.90417.0524114.5577-3.69758.7558-1.5622-1.02522.59961.59991.5258-3.15170.2658-0.84350.0364-0.02770.0822-0.0108-0.04560.0013-0.002732.078945.74139.6497
41.537-0.5962-0.38191.09370.09611.5418-0.09580.0459-0.01590.05440.04240.04780.16990.0450.05350.04810.0916-0.0005-0.0991-0.0115-0.053526.11331.093417.4564
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11E01
22A1 - 3021 - 302
33A303 - 314303 - 314
44A315 - 414315 - 414

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