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- PDB-5ibu: 6652 Fab (unbound) -

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Basic information

Entry
Database: PDB / ID: 5ibu
Title6652 Fab (unbound)
Components
  • 6652 Heavy Chain
  • 6652 Light Chain
KeywordsIMMUNE SYSTEM / antibody / influenza / unbound
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsRaymond, D.D. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat. Med. / Year: 2016
Title: Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain.
Authors: Raymond, D.D. / Stewart, S.M. / Lee, J. / Ferdman, J. / Bajic, G. / Do, K.T. / Ernandes, M.J. / Suphaphiphat, P. / Settembre, E.C. / Dormitzer, P.R. / Del Giudice, G. / Finco, O. / Kang, T.H. ...Authors: Raymond, D.D. / Stewart, S.M. / Lee, J. / Ferdman, J. / Bajic, G. / Do, K.T. / Ernandes, M.J. / Suphaphiphat, P. / Settembre, E.C. / Dormitzer, P.R. / Del Giudice, G. / Finco, O. / Kang, T.H. / Ippolito, G.C. / Georgiou, G. / Kepler, T.B. / Haynes, B.F. / Moody, M.A. / Liao, H.X. / Schmidt, A.G. / Harrison, S.C.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
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
B: 6652 Light Chain
G: 6652 Heavy Chain
H: 6652 Heavy Chain
L: 6652 Light Chain


Theoretical massNumber of molelcules
Total (without water)96,5404
Polymers96,5404
Non-polymers00
Water19,1861065
1
B: 6652 Light Chain
G: 6652 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)48,2702
Polymers48,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-33 kcal/mol
Surface area20390 Å2
MethodPISA
2
H: 6652 Heavy Chain
L: 6652 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,2702
Polymers48,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-27 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.630, 89.570, 117.750
Angle α, β, γ (deg.)90.000, 93.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 6652 Light Chain


Mass: 23613.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 6652 Heavy Chain


Mass: 24656.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M NaCitrate pH 5.6, 20% PEG 4K, 20% Isopropanol and 10% glycerol as a cryoprotectant

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Data collection

DiffractionMean temperature: 173.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999973 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999973 Å / Relative weight: 1
ReflectionResolution: 1.71→44.78 Å / Num. obs: 103494 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 25.65 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.71-1.811.1381.02174.7
1.81-1.931.0732.65199.4
1.93-2.090.5085.6199.7
2.09-2.290.2958.35199.7
2.29-2.560.17911.45199.5
2.56-2.950.09216.71199.1
2.95-3.610.04424.35197.9
3.61-5.090.0332.67196.4
5.09-44.780.02340.89196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HP0,4FQL

4hp0

4fql


Resolution: 1.71→44.78 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5175 5 %RANDOM
Rwork0.21 ---
obs0.212 103492 95.2 %-
Displacement parametersBiso max: 116.43 Å2 / Biso mean: 25.9 Å2 / Biso min: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1--4.8078 Å20 Å20.7645 Å2
2--0.9937 Å20 Å2
3---3.8142 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.71→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6671 0 0 1065 7736
Biso mean---36.51 -
Num. residues----873
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2256SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes999HARMONIC5
X-RAY DIFFRACTIONt_it6844HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion894SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8422SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6844HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9314HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion16.49
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 238 5 %
Rwork0.459 4525 -
all-4763 -
obs--59.15 %

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