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- PDB-5esa: Crystal structure of anti-HCV E2 antibody HC84-26 -

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Basic information

Entry
Database: PDB / ID: 5esa
TitleCrystal structure of anti-HCV E2 antibody HC84-26
Components
  • Anti-HCV E2 glycoprotein Fab heavy chain
  • Anti-HCV E2 glycoprotein Fab light chain
KeywordsIMMUNE SYSTEM / Hepatitis C virus / E2 glycoprotein / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGao, M. / Mariuzza, R.
CitationJournal: To be Published
Title: Crystal structure of anti-HCV E2 antibody HC84-26
Authors: Gao, M. / Mariuzza, R.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-HCV E2 glycoprotein Fab heavy chain
B: Anti-HCV E2 glycoprotein Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,4702
Polymers46,4702
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-26 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.736, 69.806, 87.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Anti-HCV E2 glycoprotein Fab heavy chain


Mass: 23087.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Antibody Anti-HCV E2 glycoprotein Fab light chain


Mass: 23381.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% w/v PEG1000, 0.1 M sodium cacodylate/HCl, pH 6.5, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→37.17 Å / Num. obs: 12733 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.8
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37.17 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 631 4.96 %Random selection
Rwork0.1845 12100 --
obs0.1879 12731 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.81 Å2 / Biso mean: 27.8809 Å2 / Biso min: 8.53 Å2
Refinement stepCycle: final / Resolution: 2.6→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 0 90 3311
Biso mean---23.57 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113302
X-RAY DIFFRACTIONf_angle_d1.3234502
X-RAY DIFFRACTIONf_chiral_restr0.076513
X-RAY DIFFRACTIONf_plane_restr0.007574
X-RAY DIFFRACTIONf_dihedral_angle_d15.0261163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6001-2.80080.36951300.242623662496
2.8008-3.08250.31861140.232223852499
3.0825-3.52820.28321130.197624012514
3.5282-4.4440.22281400.161124072547
4.444-37.17470.18721340.151525412675

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