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- PDB-5jo4: Antibody Fab Fragment Complex -

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Basic information

Entry
Database: PDB / ID: 5jo4
TitleAntibody Fab Fragment Complex
Components
  • D80 Fab Heavy Chain
  • D80 Fab Light Chain
  • G6 Fab Heavy Chain
  • G6 Fab Light Chain
KeywordsIMMUNE SYSTEM / Antibody Fab Fragment Complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.53 Å
AuthorsZhang, Z. / Prachanronarong, K.P. / Marasco, W.A. / Schiffer, C.A.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Defense Advanced Research Projects AgencyDARPA-BAA-10-93 United States
Department of Defense (DOD, United States)HR0011-11-C-0095 United States
CitationJournal: To Be Published
Title: Structural Basis of an Influenza Hemagglutinin Stem-Directed Antibody Retaining the G6 Idiotype
Authors: Avnir, Y. / Zhang, Z. / Prachanronarong, K. / Schiffer, C.A. / Marasco, W.A.
History
DepositionMay 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: D80 Fab Heavy Chain
B: D80 Fab Light Chain
C: G6 Fab Heavy Chain
D: G6 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3415
Polymers94,2454
Non-polymers961
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-66 kcal/mol
Surface area37930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.160, 50.780, 139.740
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 4 types, 4 molecules ABCD

#1: Antibody D80 Fab Heavy Chain


Mass: 24037.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody D80 Fab Light Chain


Mass: 23409.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody G6 Fab Heavy Chain


Mass: 23547.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody G6 Fab Light Chain


Mass: 23249.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 2 types, 223 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NH4SO4, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.5 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.53→50.39 Å / Num. obs: 33988 / % possible obs: 97 % / Redundancy: 4.4 % / Net I/σ(I): 14.35

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Processing

Software
NameVersionClassification
PHENIXdev_2037refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementResolution: 2.53→50.39 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.54
RfactorNum. reflection% reflection
Rfree0.2478 1968 5.94 %
Rwork0.1966 --
obs0.1997 33149 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.53→50.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 5 222 6757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016689
X-RAY DIFFRACTIONf_angle_d1.3599105
X-RAY DIFFRACTIONf_dihedral_angle_d12.9984001
X-RAY DIFFRACTIONf_chiral_restr0.0541032
X-RAY DIFFRACTIONf_plane_restr0.0061160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5301-2.59330.32881340.28452045X-RAY DIFFRACTION91
2.5933-2.66350.36351410.26092138X-RAY DIFFRACTION94
2.6635-2.74180.30221360.24572151X-RAY DIFFRACTION95
2.7418-2.83030.28671310.23612178X-RAY DIFFRACTION95
2.8303-2.93150.33351390.24532182X-RAY DIFFRACTION96
2.9315-3.04880.28441390.22862201X-RAY DIFFRACTION97
3.0488-3.18760.29551390.23312236X-RAY DIFFRACTION98
3.1876-3.35560.26621350.22032238X-RAY DIFFRACTION99
3.3556-3.56580.27821480.21442244X-RAY DIFFRACTION99
3.5658-3.8410.23611430.20472276X-RAY DIFFRACTION99
3.841-4.22730.22731470.17412308X-RAY DIFFRACTION99
4.2273-4.83860.18091400.14052272X-RAY DIFFRACTION100
4.8386-6.09450.19781440.15832315X-RAY DIFFRACTION100
6.0945-50.40020.22011520.17692397X-RAY DIFFRACTION99

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