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- PDB-1j7e: A Structural Basis for the Unique Binding Features of the Human V... -

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Basic information

Entry
Database: PDB / ID: 1j7e
TitleA Structural Basis for the Unique Binding Features of the Human Vitamin D-binding Protein
Componentsvitamin D binding protein
KeywordsTRANSPORT / LIGAND BINDING PROTEIN / vitamin D binding / vitamin D3 analogue / Group-specific component / Gc-globulin
Function / homology
Function and homology information


vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / lysosomal lumen / actin binding / blood microparticle / extracellular space ...vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / lysosomal lumen / actin binding / blood microparticle / extracellular space / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Vitamin D-binding protein / Vitamin D binding protein, domain III / Vitamin D binding protein, domain III / Serum Albumin; Chain A, Domain 1 - #10 / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. ...Vitamin D-binding protein / Vitamin D binding protein, domain III / Vitamin D binding protein, domain III / Serum Albumin; Chain A, Domain 1 - #10 / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-JY / OLEIC ACID / Vitamin D-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsVerboven, C. / Rabijns, A. / De Maeyer, M. / Van Baelen, H. / Bouillon, R. / De Ranter, C.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: A structural basis for the unique binding features of the human vitamin D-binding protein.
Authors: Verboven, C. / Rabijns, A. / De Maeyer, M. / Van Baelen, H. / Bouillon, R. / De Ranter, C.
History
DepositionMay 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: vitamin D binding protein
B: vitamin D binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2157
Polymers102,5552
Non-polymers1,6615
Water4,432246
1
A: vitamin D binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9663
Polymers51,2771
Non-polymers6892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: vitamin D binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2494
Polymers51,2771
Non-polymers9723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.977, 131.977, 73.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein vitamin D binding protein


Mass: 51277.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02774
#2: Chemical ChemComp-JY / 3-(2-{4-[2-(5-HYDROXY-2-METHYLENE-CYCLOHEXYLIDENE)-ETHYLIDENE]-7A-METHYL-OCTAHYDRO-INDEN-1-YL}-PROPYL)-PHENOL / 22-(M-HYDROXYPHENYL)-23,24,25,26,27-PENTANOR VITAMIN D3


Mass: 406.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H38O2
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 400, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.912 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 2000 / Details: toroidal mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.37→30 Å / Num. obs: 51580 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 15.9
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2503 / Rsym value: 0.539 / % possible all: 99.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J78

1j78


Resolution: 2.55→29.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 664800.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: There are two molecules in the asymmetric unit: chain A and B. For chain A residues 1-6, 60-68, 81-83, 99-102 and 458 and for chain B residues 1-2, 98-104, and 457-458 are disordered and ...Details: There are two molecules in the asymmetric unit: chain A and B. For chain A residues 1-6, 60-68, 81-83, 99-102 and 458 and for chain B residues 1-2, 98-104, and 457-458 are disordered and have not been included in the model.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1925 4.9 %RANDOM
Rwork0.213 ---
all-39559 --
obs-39559 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.04 Å2 / ksol: 0.327566 e/Å3
Displacement parametersBiso mean: 63.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20 Å2
2---1.55 Å20 Å2
3---3.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.55→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 120 246 7170
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it3.951.5
X-RAY DIFFRACTIONc_mcangle_it5.62
X-RAY DIFFRACTIONc_scbond_it7.12
X-RAY DIFFRACTIONc_scangle_it8.732.5
LS refinement shellResolution: 2.55→2.67 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 153 3.2 %
Rwork0.241 4583 -
obs-5524 92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2JY.PARJY.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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