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- PDB-2v3p: Crystallographic analysis of beta-axial ligand substitutions in c... -

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Basic information

Entry
Database: PDB / ID: 2v3p
TitleCrystallographic analysis of beta-axial ligand substitutions in cobalamin bound to transcobalamin
ComponentsTRANSCOBALAMIN-2
KeywordsTRANSPORT PROTEIN / ION TRANSPORT / VITAMIN B12 TRANSPORT PROTEIN / BETA LIGAND SUBSTITUTION
Function / homology
Function and homology information


Transport of RCbl within the body / cobalamin transport / cobalt ion 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 ...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 / SULFITE ION / Transcobalamin-2
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWuerges, J. / Geremia, S. / Randaccio, L.
CitationJournal: Iubmb Life / Year: 2007
Title: Vitamin B12 Transport Proteins: Crystallographic Analysis of Beta-Axial Ligand Substitutions in Cobalamin Bound to Transcobalamin.
Authors: Wuerges, J. / Geremia, S. / Fedosov, S.N. / Randaccio, L.
History
DepositionJun 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 31, 2012Group: Non-polymer description / Refinement description
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)47,8326
Polymers46,3151
Non-polymers1,5175
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.390, 100.390, 129.742
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-2 / TCII / TC II / TRANSCOBALAMIN II


Mass: 46315.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Organ: BLOOD / Plasmid: PPICZ(ALPHA)-LB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): SMD 1168 / References: UniProt: Q9XSC9
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.1 Å3/Da / Density % sol: 69.9 % / Description: NONE
Crystal growpH: 8.5
Details: THE PROTEIN AT 0.5 MM IN 1 M NACL, 0.1 M TRIS, PH 7.5 CRYSTALLIZED FROM 28% PEG 8000, 0.2 M MAGNESIUM ACETATE, 0.1 M TRIS PH 8.5, 20% 2-METHYL-2, 4-PENTADIOL, 40 MM (NH4)2SO3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 2007
RadiationMonochromator: DOUBLE CRYSTAL SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.9→29.3 Å / Num. obs: 16711 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BBC

2bbc


Resolution: 2.9→28.98 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 25.622 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.675 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO ACIDS FROM LYS168 TO VAL176 WERE NOT MODELLED DUE TO DISORDER. HIS175 AS UPPER AXIAL LIGAND OF COBALAMIN HAS BEEN DISPLACED BY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO ACIDS FROM LYS168 TO VAL176 WERE NOT MODELLED DUE TO DISORDER. HIS175 AS UPPER AXIAL LIGAND OF COBALAMIN HAS BEEN DISPLACED BY EXTERNALLY SUPPLIED SULFITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 640 3.83 %RANDOM
Rwork0.194 ---
obs0.196 16697 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 98 120 3396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223348
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3332.0254566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45723.776143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61215586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7971526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022512
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21561
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22294
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6671.52067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15823248
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.24431415
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2084.51318
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 44
Rwork0.311 1164
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6657-0.8281-2.14640.1210.31370.8131-0.07780.0625-0.6763-0.12930.08450.3680.5236-0.2907-0.00670.18320.00860.016-0.0376-0.0790.102113.243437.936716.8046
21.72080.10820.6972.70710.38123.4763-0.08950.0668-0.09910.1476-0.05770.2732-0.0088-0.31860.1472-0.08660.09730.075-0.0445-0.0468-0.0523.954547.640819.6303
327.3067-46.32772.974981.1208-3.21321.6574-3.4544-1.99413.17474.6923.7904-1.8526-0.1397-1.9716-0.3360.71380.5494-0.03020.9632-0.03021.314332.570446.221739.9966
44.1361-1.38350.05544.03940.40023.651-0.10980.1402-0.1172-0.0157-0.02380.12480.19050.03740.13360.01550.08150.0046-0.1189-0.0208-0.052126.376731.232917.5864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1
2X-RAY DIFFRACTION2A2 - 302
3X-RAY DIFFRACTION3A303 - 314
4X-RAY DIFFRACTION4A315 - 414

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