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- PDB-5jmr: X-ray structure of the furin inhibitory antibody Nb14 -

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Basic information

Entry
Database: PDB / ID: 5jmr
TitleX-ray structure of the furin inhibitory antibody Nb14
Componentscamelid VHH fragment
KeywordsIMMUNE SYSTEM / camelid / antibody / inhibitor / furin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDahms, S.O. / Than, M.E.
CitationJournal: Sci Rep / Year: 2016
Title: The structure of a furin-antibody complex explains non-competitive inhibition by steric exclusion of substrate conformers.
Authors: Dahms, S.O. / Creemers, J.W. / Schaub, Y. / Bourenkov, G.P. / Zogg, T. / Brandstetter, H. / Than, M.E.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Structure summary
Revision 1.2Oct 16, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: camelid VHH fragment
B: camelid VHH fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3634
Polymers27,2922
Non-polymers712
Water2,360131
1
A: camelid VHH fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6822
Polymers13,6461
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: camelid VHH fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6822
Polymers13,6461
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.411, 91.411, 211.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

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Components

#1: Antibody camelid VHH fragment


Mass: 13646.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 4.04 Å3/Da / Density % sol: 69.58 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 10 mM Hepes, pH 7.5, 100 mM NaCl and 1mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.27→35.356 Å / Num. obs: 21253 / % possible obs: 99.7 % / Redundancy: 6.6 % / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OP9

1op9


Resolution: 2.27→35.356 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 1065 5.04 %
Rwork0.1897 --
obs0.1911 21130 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→35.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 2 131 1897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011838
X-RAY DIFFRACTIONf_angle_d1.1542496
X-RAY DIFFRACTIONf_dihedral_angle_d15.45644
X-RAY DIFFRACTIONf_chiral_restr0.048265
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2701-2.37340.27261420.24582456X-RAY DIFFRACTION100
2.3734-2.49850.26831420.24512435X-RAY DIFFRACTION100
2.4985-2.6550.3051420.23082457X-RAY DIFFRACTION100
2.655-2.85990.256710.2192544X-RAY DIFFRACTION100
2.8599-3.14750.25281420.21292482X-RAY DIFFRACTION100
3.1475-3.60260.23171420.17712489X-RAY DIFFRACTION100
3.6026-4.53740.16141420.15182527X-RAY DIFFRACTION100
4.5374-35.36020.1821420.1742675X-RAY DIFFRACTION100

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