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- PDB-2i9l: Structure of Fab 7D11 from a neutralizing antibody against the po... -

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Basic information

Entry
Database: PDB / ID: 2i9l
TitleStructure of Fab 7D11 from a neutralizing antibody against the poxvirus L1 protein
Components
  • Antibody 7D11 heavy chain
  • Antibody 7D11 light chain
  • Virion membrane protein M25
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Neutralizing antibody / Poxvirus / antibody complex / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Virion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Entry-fusion complex associated protein OPG095
Similarity search - Component
Biological speciesVaccinia virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSu, H.P. / Golden, J.W. / Gittis, A.G. / Moss, B. / Hooper, J.W. / Garboczi, D.N.
CitationJournal: Virology / Year: 2007
Title: Structural basis for the binding of the neutralizing antibody, 7D11, to the poxvirus L1 protein
Authors: Su, H.-P. / Golden, J.W. / Gittis, A.G. / Hooper, J.W. / Garboczi, D.N.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: Antibody 7D11 light chain
B: Antibody 7D11 heavy chain
C: Antibody 7D11 light chain
D: Antibody 7D11 heavy chain
E: Antibody 7D11 light chain
F: Antibody 7D11 heavy chain
G: Antibody 7D11 light chain
H: Antibody 7D11 heavy chain
I: Virion membrane protein M25
J: Virion membrane protein M25
K: Virion membrane protein M25
L: Virion membrane protein M25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,24620
Polymers269,50912
Non-polymers7378
Water25214
1
A: Antibody 7D11 light chain
B: Antibody 7D11 heavy chain
I: Virion membrane protein M25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5615
Polymers67,3773
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Antibody 7D11 light chain
D: Antibody 7D11 heavy chain
J: Virion membrane protein M25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4694
Polymers67,3773
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Antibody 7D11 light chain
F: Antibody 7D11 heavy chain
K: Virion membrane protein M25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7467
Polymers67,3773
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Antibody 7D11 light chain
H: Antibody 7D11 heavy chain
L: Virion membrane protein M25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4694
Polymers67,3773
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.770, 85.561, 211.843
Angle α, β, γ (deg.)90.00, 119.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
Antibody 7D11 light chain


Mass: 24175.852 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Antibody light chain isolated from a hybridoma / Source: (natural) Mus musculus (house mouse)
#2: Antibody
Antibody 7D11 heavy chain


Mass: 23668.525 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Antibody heavy chain isolated from a hybridoma / Source: (natural) Mus musculus (house mouse)
#3: Protein
Virion membrane protein M25


Mass: 19532.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: Western Reserve / Gene: l1r / Plasmid: pNAN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) - RIL / References: UniProt: P07612
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 298 K / pH: 8
Details: 10% PEG 10000, 0.1M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2005
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 61289 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.464 / % possible all: 99.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.1 Å46.05 Å
Translation3.1 Å46.05 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YPY, 1YMH

1ypy

1ymh


Resolution: 3.1→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3109 5 %RANDOM
Rwork0.24 ---
obs0.24 61228 98.4 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 39.19 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18612 0 48 14 18674
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1891.5
X-RAY DIFFRACTIONc_mcangle_it2.1312
X-RAY DIFFRACTIONc_scbond_it1.642
X-RAY DIFFRACTIONc_scangle_it2.6542.5
LS refinement shellResolution: 3.1→3.12 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.323 64
Rwork0.355 1015
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION3GOL_XPLOR_PAR.TXT

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