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- PDB-1j78: Crystallographic analysis of the human vitamin D binding protein -

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Basic information

Entry
Database: PDB / ID: 1j78
TitleCrystallographic analysis of the human vitamin D binding protein
Componentsvitamin D binding protein
KeywordsTRANSPORT / LIGAND BINDING PROTEIN / plasma protein / vitamin D binding / actin binding / fatty acid binding / GC-globulin / Group-specific component
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
OLEIC ACID / Chem-VDY / Vitamin D-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / COMBINED MAD, MIRAS / Resolution: 2.31 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

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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)103,8036
Polymers102,5552
Non-polymers1,2484
Water5,386299
1
A: vitamin D binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5602
Polymers51,2771
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: vitamin D binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2434
Polymers51,2771
Non-polymers9663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.248, 132.248, 73.179
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-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-VDY / 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL / 25-HYDROXYVITAMIN D3 / Calcifediol


Mass: 400.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 60.56 %
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
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Verboven, C.C., (1995) J. Steroid Biochem. Mol. Biol., 54, 11.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 %(v/v)PEG4001reservoir
20.1 Macetate1reservoirpH4.6
330 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9116 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 1999 / Details: Bent mirror
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2.31→30 Å / Num. all: 55933 / Num. obs: 55444 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 50.6 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 22.7
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2766 / Rsym value: 0.209 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 187531
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: COMBINED MAD, MIRAS / Resolution: 2.31→29.38 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1255175.19 / 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 1-12, 60-67, 99-102 and 458 and for chain B residues 1-2, 98-104 and 457-458 are disordered and have not ...Details: There are two molecules in the asymmetric unit: chain A and B. For chain A residues 1-12, 60-67, 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
Rfree0.252 2221 4 %RANDOM
Rwork0.22 ---
all-55159 --
obs-55159 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.26 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 60.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å20 Å2
2--3.24 Å20 Å2
3----6.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.31→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 89 299 7137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it4.091.5
X-RAY DIFFRACTIONc_mcangle_it5.612
X-RAY DIFFRACTIONc_scbond_it6.722
X-RAY DIFFRACTIONc_scangle_it8.432.5
LS refinement shellResolution: 2.31→2.42 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.351 305 4.5 %
Rwork0.29 6535 -
obs-6535 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMLINO.TOP
X-RAY DIFFRACTION3LINO.PARWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 53194 / σ(F): 0 / Num. reflection Rfree: 2236 / % reflection Rfree: 4 % / Rfactor obs: 0.2201 / Rfactor Rfree: 0.2518 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 60.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it4.091.5
X-RAY DIFFRACTIONc_scbond_it6.722
X-RAY DIFFRACTIONc_mcangle_it5.612
X-RAY DIFFRACTIONc_scangle_it8.432.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.29

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