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- PDB-1kw2: CRYSTAL STRUCTURE OF UNCOMPLEXED VITAMIN D-BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1kw2
TitleCRYSTAL STRUCTURE OF UNCOMPLEXED VITAMIN D-BINDING PROTEIN
ComponentsVitamin D-binding protein
KeywordsTRANSPORT PROTEIN / DBP / vitamin D-binding protein / Actin scavenger system / Actin-binding protein
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 / cytoplasm / cytosol
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
Vitamin D-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOtterbein, L.R. / Dominguez, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structures of the vitamin D-binding protein and its complex with actin: structural basis of the actin-scavenger system.
Authors: Otterbein, L.R. / Cosio, C. / Graceffa, P. / Dominguez, R.
History
DepositionJan 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin D-binding protein
B: Vitamin D-binding protein


Theoretical massNumber of molelcules
Total (without water)102,6112
Polymers102,6112
Non-polymers00
Water5,999333
1
A: Vitamin D-binding protein


Theoretical massNumber of molelcules
Total (without water)51,3051
Polymers51,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vitamin D-binding protein


Theoretical massNumber of molelcules
Total (without water)51,3051
Polymers51,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.925, 133.925, 73.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsTwo molecules are present in the asymetric unit. Molecule A is the best one.

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Components

#1: Protein Vitamin D-binding protein / DBP / Group-specific component / GC-globulin


Mass: 51305.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02774
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 3.2 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 200, 28%, Sodium Acetate, 0.1M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
228 %PEG2001reservoir
3100 mMsodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2001 / Details: BENT CYLINDRICAL Si-MIRROR (RH coating)
RadiationMonochromator: Si (III)DOUBLE CRYSTAL,L=1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→60 Å / Num. all: 67333 / Num. obs: 67333 / % possible obs: 94.9 % / Redundancy: 15.5 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.7
Reflection shellResolution: 2.15→2.32 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 10.2 / Num. unique all: 16595 / % possible all: 81.2
Reflection
*PLUS
Lowest resolution: 60 Å / Num. obs: 67175 / Num. measured all: 1041011
Reflection shell
*PLUS
% possible obs: 81.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VITAMIN D-BINDING PROTEIN COMPLEXED WITH ACTIN PDB 1KXP

1kxp


Resolution: 2.15→60 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3419 5 %RANDOM
Rwork0.218 ---
all-67333 --
obs-67333 94.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.15→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7075 0 0 333 7408
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d18.67
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.15→2.32 Å
RfactorNum. reflection% reflection
Rfree0.287 893 5 %
Rwork0.262 16595 -
obs-16959 81.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARM
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.67
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rwork: 0.251

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