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- PDB-1kxp: CRYSTAL STRUCTURE OF HUMAN VITAMIN D-BINDING PROTEIN IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1kxp
TitleCRYSTAL STRUCTURE OF HUMAN VITAMIN D-BINDING PROTEIN IN COMPLEX WITH SKELETAL ACTIN
Components
  • ACTIN,ALPHA SKELETAL MUSCLE
  • HUMAN VITAMIN D-BINDING PROTEIN
KeywordsCONTRACTILE PROTEIN/PROTEIN BINDING / DBP / vitamin D-binding protein / Actin Scavenger system / Actin-Binding Protein / CONTRACTILE PROTEIN-PROTEIN BINDING COMPLEX
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 / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration ...vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / lysosomal lumen / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / actin binding / blood microparticle / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Vitamin D-binding protein / Vitamin D binding protein, domain III / Vitamin D binding protein, domain III / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Serum Albumin; Chain A, Domain 1 - #10 / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like ...Vitamin D-binding protein / Vitamin D binding protein, domain III / Vitamin D binding protein, domain III / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / 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 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Vitamin D-binding protein / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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
DepositionFeb 1, 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: Derived calculations / Version format compliance
Revision 1.3Sep 18, 2013Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIN,ALPHA SKELETAL MUSCLE
D: HUMAN VITAMIN D-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6994
Polymers93,1682
Non-polymers5312
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-32 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.758, 87.364, 162.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ACTIN,ALPHA SKELETAL MUSCLE / ALPHA-ACTIN 1


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MUSCLE / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein HUMAN VITAMIN D-BINDING PROTEIN / / DBP / VDB / GROUP-SPECIFIC COMPONENT / GC-GLOBULIN


Mass: 51305.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SERUM / Source: (natural) Homo sapiens (human) / References: UniProt: P02774
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Peg 8K 12%, Magnesium Acetate 200mM, Sodium Cacodylate 100 mM, Glycerol 20%, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1droppH7.6
20.6 mMATP1drop
30.5 mMbeta-mercaptoethanol1drop
40.2 mM1dropCaCl2
520 mg/mlprotein1drop
611 %PEG120001reservoir
7200 mMmagnesium acetate1reservoir
8100 mMsodium cacodylate1reservoirpH6.6
920 %glycerol1reservoir

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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: 2.1→40 Å / Num. all: 67774 / Num. obs: 67458 / % possible obs: 99.8 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 23.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 11.2 / Num. unique all: 6596 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 1064049
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 98.8 % / Redundancy: 11 % / Mean I/σ(I) obs: 9.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.1→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3424 5 %RANDOM
Rwork0.217 ---
all-67774 --
obs-67774 99.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6167 0 32 388 6587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d20.64
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection
Rfree0.249 819
Rwork0.242 -
obs-15817
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_deg20.64
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Highest resolution: 2.1 Å

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