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- PDB-5jqd: Antibody Fab Fragment -

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Basic information

Entry
Database: PDB / ID: 5jqd
TitleAntibody Fab Fragment
Components
  • D80 Fab Fragment Heavy Chain
  • D80 Fab Fragment Light Chain
KeywordsIMMUNE SYSTEM / Antibody Fab Fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.591 Å
AuthorsZhang, Z. / Prachanronarong, K. / Gellatly, K. / Marasco, W.A. / Schiffer, C.A.
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. / Gellatly, K. / Schiffer, C.A. / Marasco, W.A.
History
DepositionMay 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D80 Fab Fragment Light Chain
B: D80 Fab Fragment Light Chain
C: D80 Fab Fragment Heavy Chain
D: D80 Fab Fragment Heavy Chain


Theoretical massNumber of molelcules
Total (without water)94,8964
Polymers94,8964
Non-polymers00
Water1,67593
1
A: D80 Fab Fragment Light Chain
D: D80 Fab Fragment Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,4482
Polymers47,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-21 kcal/mol
Surface area19200 Å2
MethodPISA
2
B: D80 Fab Fragment Light Chain
C: D80 Fab Fragment Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,4482
Polymers47,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-22 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.055, 91.577, 106.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody D80 Fab Fragment Light Chain


Mass: 23409.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody D80 Fab Fragment Heavy Chain


Mass: 24037.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2 M CaCl2, 0.1 M Tris pH 8.4

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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: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.59→46.12 Å / Num. obs: 26407 / % possible obs: 95 % / Redundancy: 5 % / Net I/σ(I): 11.16

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.591→46.117 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1273 4.82 %
Rwork0.2115 --
obs0.213 26404 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.591→46.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6329 0 0 93 6422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056487
X-RAY DIFFRACTIONf_angle_d0.7458844
X-RAY DIFFRACTIONf_dihedral_angle_d14.0053857
X-RAY DIFFRACTIONf_chiral_restr0.0461007
X-RAY DIFFRACTIONf_plane_restr0.0051135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.591-2.69470.2961400.29032749X-RAY DIFFRACTION95
2.6947-2.81730.33051400.26282800X-RAY DIFFRACTION97
2.8173-2.96580.29751410.24752799X-RAY DIFFRACTION96
2.9658-3.15160.28841340.23792795X-RAY DIFFRACTION96
3.1516-3.39490.25041560.22572776X-RAY DIFFRACTION96
3.3949-3.73640.2551250.20512785X-RAY DIFFRACTION95
3.7364-4.27670.23011640.1892780X-RAY DIFFRACTION95
4.2767-5.38690.18731090.16612823X-RAY DIFFRACTION94
5.3869-46.12420.21861640.22072824X-RAY DIFFRACTION92

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