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- PDB-6x9x: Crystal structure of Fab fragment of Anti-HCV E2 antibody (HC84.26) -

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Basic information

Entry
Database: PDB / ID: 6x9x
TitleCrystal structure of Fab fragment of Anti-HCV E2 antibody (HC84.26)
Components
  • HC84.26 Fab Heavy Chain
  • HC84.26 Fab Light Chain
KeywordsANTIVIRAL PROTEIN / IMMUNE SYSTEM / anti HCV E2 / Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShahid, S. / Mariuzza, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI132213 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Crystal Structure of a Bivalent Antibody Fab Fragment.
Authors: Shahid, S. / Gao, M. / Travis Gallagher, D. / Pozharski, E. / Brinson, R.G. / Keck, Z.Y. / Foung, S.K.H. / Fuerst, T.R. / Mariuzza, R.A.
History
DepositionJun 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HC84.26 Fab Heavy Chain
B: HC84.26 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1565
Polymers47,9732
Non-polymers1833
Water5,999333
1
A: HC84.26 Fab Heavy Chain
B: HC84.26 Fab Light Chain
hetero molecules

A: HC84.26 Fab Heavy Chain
B: HC84.26 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,31310
Polymers95,9474
Non-polymers3666
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7880 Å2
ΔGint-37 kcal/mol
Surface area39510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.535, 113.699, 122.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21A-556-

HOH

31B-447-

HOH

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Components

#1: Antibody HC84.26 Fab Heavy Chain


Mass: 24962.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human)
#2: Antibody HC84.26 Fab Light Chain


Mass: 23010.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.4 M Ammonium Acetate, 20% PEG 2000 MME, Cryoprotectant-Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 53599 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Net I/σ(I): 26.41
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 5293 / CC1/2: 0.771 / CC star: 0.933 / Rpim(I) all: 0.326 / Rrim(I) all: 0.728 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ESA

5esa


Resolution: 1.8→34.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.544 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20966 2648 4.9 %RANDOM
Rwork0.17839 ---
obs0.17993 50913 99.68 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å20 Å2
2---0.31 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 12 333 3529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193291
X-RAY DIFFRACTIONr_bond_other_d0.0010.022930
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.8754487
X-RAY DIFFRACTIONr_angle_other_deg1.0722.9266852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.6735.632451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46124.286119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09715496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4041511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
X-RAY DIFFRACTIONr_mcbond_it2.4292.2751701
X-RAY DIFFRACTIONr_mcbond_other2.4282.2711699
X-RAY DIFFRACTIONr_mcangle_it3.7953.3852123
X-RAY DIFFRACTIONr_mcangle_other3.7953.3882124
X-RAY DIFFRACTIONr_scbond_it3.3362.5911590
X-RAY DIFFRACTIONr_scbond_other3.3372.5941591
X-RAY DIFFRACTIONr_scangle_other5.0613.7162362
X-RAY DIFFRACTIONr_long_range_B_refined7.92628.4393579
X-RAY DIFFRACTIONr_long_range_B_other7.86427.4733484
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 222 -
Rwork0.28 3648 -
obs--98.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8934-0.9484-0.14422.62140.39490.44570.0266-0.037-0.02180.0235-0.01090.01770.0187-0.0847-0.01560.01180.0018-0.0170.11760.00520.03075.67463.38137.096
21.709-0.291-1.57061.2078-0.10833.4657-0.1618-0.0343-0.05310.0520.03680.04990.3351-0.30470.12490.05580.01290.00220.1586-0.03160.022215.35134.03543.244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 221
2X-RAY DIFFRACTION2B1 - 213

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