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- PDB-7np9: Structure of the human CR3 - CD11bCD18 specific nanobody hCR3Nb1 -

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Basic information

Entry
Database: PDB / ID: 7np9
TitleStructure of the human CR3 - CD11bCD18 specific nanobody hCR3Nb1
ComponentshCR3Nb1
KeywordsIMMUNE SYSTEM / nanobody / antibody / integrin receptor / complement / phagocytosis / inhibitor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsJensen, R.K. / Andersen, G.R.
Funding support Denmark, 2items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Novo Nordisk FoundationNNF18OC0052105 Denmark
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural insights into the function-modulating effects of nanobody binding to the integrin receptor alpha M beta 2.
Authors: Jensen, R.K. / Pedersen, H. / Lorentzen, J. / Laursen, N.S. / Vorup-Jensen, T. / Andersen, G.R.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: hCR3Nb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3203
Polymers14,1281
Non-polymers1922
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.781, 82.781, 72.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-340-

HOH

21C-403-

HOH

31C-405-

HOH

41C-429-

HOH

51C-431-

HOH

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Components

#1: Antibody hCR3Nb1


Mass: 14127.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 1.5 M AmSO4, 0.1 M BIS-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.14→54.52 Å / Num. obs: 44396 / % possible obs: 96.37 % / Redundancy: 45 % / Biso Wilson estimate: 12.24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1591 / Net I/σ(I): 21.5
Reflection shellResolution: 1.14→1.181 Å / Num. unique obs: 3194 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHG

6ehg


Resolution: 1.14→54.52 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1669 2008 4.53 %
Rwork0.1462 42323 -
obs0.1472 44331 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.04 Å2
Refinement stepCycle: LAST / Resolution: 1.14→54.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 10 167 1110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971035
X-RAY DIFFRACTIONf_angle_d1.16341416
X-RAY DIFFRACTIONf_chiral_restr0.0933151
X-RAY DIFFRACTIONf_plane_restr0.0083184
X-RAY DIFFRACTIONf_dihedral_angle_d6.0726158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.2549850.23991782X-RAY DIFFRACTION56.63
1.17-1.20.23581390.22372939X-RAY DIFFRACTION95.15
1.2-1.230.22091450.20763062X-RAY DIFFRACTION98.28
1.23-1.270.20691450.18953063X-RAY DIFFRACTION98.34
1.27-1.320.22321460.17933062X-RAY DIFFRACTION98.65
1.32-1.370.20891470.16753091X-RAY DIFFRACTION98.9
1.37-1.430.20651470.1483093X-RAY DIFFRACTION99.08
1.43-1.510.15961470.13213097X-RAY DIFFRACTION99.17
1.51-1.60.15391480.12233130X-RAY DIFFRACTION99.67
1.6-1.730.16311490.12053133X-RAY DIFFRACTION99.61
1.73-1.90.13411490.11763146X-RAY DIFFRACTION99.73
1.9-2.180.15151500.11753169X-RAY DIFFRACTION99.94
2.18-2.740.14511520.13913213X-RAY DIFFRACTION100
2.74-54.520.16771590.15553343X-RAY DIFFRACTION99.72

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