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- PDB-2v3n: Crystallographic analysis of upper axial ligand substitutions in ... -

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Basic information

Entry
Database: PDB / ID: 2v3n
TitleCrystallographic analysis of upper axial ligand substitutions in cobalamin bound to transcobalamin
ComponentsTRANSCOBALAMIN-2
KeywordsTRANSPORT PROTEIN / COBALT / TRANSPORT / GLYCOPROTEIN / ION TRANSPORT / VITAMIN B12 TRANSPORT PROTEIN / COBALT TRANSPORT / BETA LIGAND SUBSTITUTION
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 / CYANIDE ION / Transcobalamin-2
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 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
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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET 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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7786
Polymers46,3151
Non-polymers1,4635
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.830, 100.830, 130.215
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 / / TRANSCOBALAMIN II


Mass: 46315.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (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 / Vitamin B12


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


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 4.1 Å3/Da / Density % sol: 69.9 % / Description: NONE
Crystal growpH: 8.5
Details: 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, 15 MM KCN

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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 4, 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: 2.7→20.7 Å / Num. obs: 21370 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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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: 2.73→20.7 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / SU B: 19.725 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.448 / ESU R Free: 0.291 / 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 CYANIDE.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 857 4.25 %RANDOM
Rwork0.211 ---
obs0.213 20574 99.3 %-
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: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.433 Å20.216 Å20 Å2
2--0.433 Å20 Å2
3----0.649 Å2
Refinement stepCycle: LAST / Resolution: 2.73→20.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 96 174 3448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223352
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3082.0244570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86723.776143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01115589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7151526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21550
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22293
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6611.52081
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18123254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.31931418
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2754.51315
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: 2.73→2.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.386 59
Rwork0.346 1429
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)
14.39011.7518-1.09182.0372-1.40368.21350.02460.1984-0.3412-0.3786-0.00730.29760.2415-0.2478-0.0173-0.00490.0497-0.025-0.0868-0.04050.091413.380338.460216.7576
20.8259-0.21070.1692.10860.47023.1154-0.04640.0667-0.04920.1552-0.08820.2228-0.0606-0.28680.1346-0.07280.07060.0672-0.045-0.0298-0.02734.020648.0719.5369
348.5432-73.56240.3596111.4766-0.5450.0027-1.4201-0.90394.30131.53751.8051-2.78270.963-0.95-0.3850.56670.7923-0.11980.874-0.05260.730132.27946.468840.2227
43.2899-1.2088-0.26272.92850.62852.6865-0.05750.1582-0.0783-0.0222-0.01080.07880.2290.1060.06840.03260.1121-0.0064-0.0983-0.0087-0.04426.474331.649617.6555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1001
2X-RAY DIFFRACTION2A1 - 302
3X-RAY DIFFRACTION3A303 - 314
4X-RAY DIFFRACTION4A315 - 414

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