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- PDB-6jp7: Human antibody 32D6 Fab in complex with PEG -

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Basic information

Entry
Database: PDB / ID: 6jp7
TitleHuman antibody 32D6 Fab in complex with PEG
Components
  • immunoglobulin Fab heavy chain
  • immunoglobulin Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody Fab / influenza hemagglutinin / complex structure / specific binding / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-3FX
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.909 Å
AuthorsLee, C.C. / Ko, T.P. / Lin, L.L. / Wang, A.H.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J.Biomed.Sci. / Year: 2020
Title: Structural basis of polyethylene glycol recognition by antibody.
Authors: Lee, C.C. / Su, Y.C. / Ko, T.P. / Lin, L.L. / Yang, C.Y. / Chang, S.S. / Roffler, S.R. / Wang, A.H.
History
DepositionMar 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: immunoglobulin Fab heavy chain
L: immunoglobulin Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6036
Polymers48,5642
Non-polymers1,0394
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-22 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.658, 73.658, 191.249
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-1078-

HOH

21L-1188-

HOH

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Components

#1: Antibody immunoglobulin Fab heavy chain


Mass: 25556.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody immunoglobulin Fab light chain


Mass: 23007.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-3FX / (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 600, CAPSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→30 Å / Num. obs: 47075 / % possible obs: 98.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.46
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4515 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4K

6a4k


Resolution: 1.909→29.177 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 2313 5.27 %
Rwork0.1687 --
obs0.1711 43899 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.909→29.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 53 567 4038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083594
X-RAY DIFFRACTIONf_angle_d0.9524892
X-RAY DIFFRACTIONf_dihedral_angle_d13.5672147
X-RAY DIFFRACTIONf_chiral_restr0.058547
X-RAY DIFFRACTIONf_plane_restr0.006614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9087-1.94770.2622720.21181457X-RAY DIFFRACTION55
1.9477-1.990.2761970.19451735X-RAY DIFFRACTION66
1.99-2.03630.2647850.19671943X-RAY DIFFRACTION75
2.0363-2.08720.19321120.19262350X-RAY DIFFRACTION89
2.0872-2.14360.23161300.19182537X-RAY DIFFRACTION97
2.1436-2.20670.27721340.18832629X-RAY DIFFRACTION99
2.2067-2.27790.24231440.18352643X-RAY DIFFRACTION100
2.2779-2.35930.24451630.17662592X-RAY DIFFRACTION100
2.3593-2.45370.24551530.17932648X-RAY DIFFRACTION100
2.4537-2.56530.20731420.18412585X-RAY DIFFRACTION100
2.5653-2.70050.2391900.18312588X-RAY DIFFRACTION99
2.7005-2.86950.22871550.18292612X-RAY DIFFRACTION99
2.8695-3.09090.22011470.17762620X-RAY DIFFRACTION98
3.0909-3.40150.21261370.16382628X-RAY DIFFRACTION98
3.4015-3.89270.20161490.14922638X-RAY DIFFRACTION98
3.8927-4.90060.15261460.12692608X-RAY DIFFRACTION95
4.9006-29.18010.1951570.16672773X-RAY DIFFRACTION97

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