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- PDB-5hdo: Crystal structure of a nanobody raised against urokinase-type pla... -

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Basic information

Entry
Database: PDB / ID: 5hdo
TitleCrystal structure of a nanobody raised against urokinase-type plasminogen activator
ComponentsAnti-HCV NS3/4A serine protease immoglobulin heavy chain
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / peptidase activity / blood microparticle / proteolysis
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Anti-HCV NS3/4A serine protease immoglobulin heavy chain
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsKromann-Hansen, T.
Funding support Denmark, China, 5items
OrganizationGrant numberCountry
Danish National Research Foundation26-331-6 Denmark
Natural Science Foundation of China31161130356, 31170707, 31370737 China
Lundbeck FoundationR83-A7826 Denmark
Cancer Research Foundation of 1989 Denmark
Graduate School of Science and Technology, Aarhus University Denmark
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior.
Authors: Kromann-Hansen, T. / Oldenburg, E. / Yung, K.W. / Ghassabeh, G.H. / Muyldermans, S. / Declerck, P.J. / Huang, M. / Andreasen, P.A. / Ngo, J.C.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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 13, 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: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
B: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
C: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
D: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,91812
Polymers54,3924
Non-polymers5268
Water8,287460
1
A: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6942
Polymers13,5981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7293
Polymers13,5981
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7293
Polymers13,5981
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Anti-HCV NS3/4A serine protease immoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7654
Polymers13,5981
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.830, 99.830, 127.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody
Anti-HCV NS3/4A serine protease immoglobulin heavy chain


Mass: 13597.960 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6YEF6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES, 0.2M ammonium sulphate, 30% w/v PEG 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.16→47.28 Å / Num. obs: 35146 / % possible obs: 99.94 % / Redundancy: 14.5 % / Biso Wilson estimate: 34.52 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 22.42
Reflection shellResolution: 2.16→2.237 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.18 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jvp

4jvp


Resolution: 2.16→47.277 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1767 5.03 %
Rwork0.1766 --
obs0.1786 35137 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→47.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 24 460 4219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073817
X-RAY DIFFRACTIONf_angle_d1.0935143
X-RAY DIFFRACTIONf_dihedral_angle_d12.1191343
X-RAY DIFFRACTIONf_chiral_restr0.045556
X-RAY DIFFRACTIONf_plane_restr0.004672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1601-2.21850.25731270.2122507X-RAY DIFFRACTION100
2.2185-2.28370.30571340.21752530X-RAY DIFFRACTION100
2.2837-2.35740.25541340.22524X-RAY DIFFRACTION100
2.3574-2.44170.28831420.2032516X-RAY DIFFRACTION100
2.4417-2.53950.26541140.19482548X-RAY DIFFRACTION100
2.5395-2.6550.26091540.19362530X-RAY DIFFRACTION100
2.655-2.7950.28821270.20512543X-RAY DIFFRACTION100
2.795-2.97010.24491530.18772531X-RAY DIFFRACTION100
2.9701-3.19930.20281400.19312562X-RAY DIFFRACTION100
3.1993-3.52120.23241380.16972574X-RAY DIFFRACTION100
3.5212-4.03050.20151370.15872599X-RAY DIFFRACTION100
4.0305-5.07710.14821350.1332628X-RAY DIFFRACTION100
5.0771-47.28860.18861320.18972778X-RAY DIFFRACTION99

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