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- PDB-4hgk: Shark IgNAR variable domain -

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Basic information

Entry
Database: PDB / ID: 4hgk
TitleShark IgNAR variable domain
Components
  • Serum albumin
  • shark V-NAR antibody
KeywordsIMMUNE SYSTEM / Ig-fold / human albumin
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / 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 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Squalus acanthias (spiny dogfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsOlland, A.O. / Kovalenko, O.V. / Svenson, K. / King, D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Atypical Antigen Recognition Mode of a Shark Immunoglobulin New Antigen Receptor (IgNAR) Variable Domain Characterized by Humanization and Structural Analysis.
Authors: Kovalenko, O.V. / Olland, A. / Piche-Nicholas, N. / Godbole, A. / King, D. / Svenson, K. / Calabro, V. / Muller, M.R. / Barelle, C.J. / Somers, W. / Gill, D.S. / Mosyak, L. / Tchistiakova, L.
History
DepositionOct 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
C: shark V-NAR antibody
D: shark V-NAR antibody


Theoretical massNumber of molelcules
Total (without water)161,4504
Polymers161,4504
Non-polymers00
Water70339
1
A: Serum albumin
D: shark V-NAR antibody


Theoretical massNumber of molelcules
Total (without water)80,7252
Polymers80,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
C: shark V-NAR antibody


Theoretical massNumber of molelcules
Total (without water)80,7252
Polymers80,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.980, 127.980, 151.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02768
#2: Protein shark V-NAR antibody


Mass: 14153.843 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Squalus acanthias (spiny dogfish) / Cell line (production host): COS-1 / Production host: Chlorocebus aethiops (grivet)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 16% PEG 2000 MME, 100 mM sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.04→52.055 Å / Num. all: 25935 / Num. obs: 25935 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 74.74 Å2 / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.9.3refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA2

1ha2


Resolution: 3.04→52.055 Å / Cor.coef. Fo:Fc: 0.8831 / Cor.coef. Fo:Fc free: 0.8542 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1318 5.08 %RANDOM
Rwork0.2373 ---
all0.2373 25935 --
obs0.2387 25935 92.08 %-
Displacement parametersBiso mean: 85.54 Å2
Baniso -1Baniso -2Baniso -3
1-14.7207 Å20 Å20 Å2
2--14.7207 Å20 Å2
3----29.4415 Å2
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: LAST / Resolution: 3.04→52.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9296 0 0 39 9335
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089506HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112862HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3375SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes255HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1353HARMONIC5
X-RAY DIFFRACTIONt_it9506HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion18.05
X-RAY DIFFRACTIONt_chiral_improper_torsion1232SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact10962SEMIHARMONIC4
LS refinement shellResolution: 3.04→3.16 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2653 146 5.04 %
Rwork0.262 2752 -
all0.2622 2898 -
obs--92.08 %

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