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- PDB-4xcc: Crystal structure of human 4E10 Fab crystalized in the presence o... -

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Basic information

Entry
Database: PDB / ID: 4xcc
TitleCrystal structure of human 4E10 Fab crystalized in the presence of Phosphatidylcholine (06:0 PC); I422 space group
Components
  • 4E10 Fab Heavy chain
  • 4E10 Fab light chain
KeywordsIMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 / lipid membrane / Phosphatidylcholine
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsIrimia, A. / Stanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
CitationJournal: Immunity / Year: 2016
Title: Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10.
Authors: Irimia, A. / Sarkar, A. / Stanfield, R.L. / Wilson, I.A.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 4E10 Fab light chain
H: 4E10 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6683
Polymers47,5762
Non-polymers921
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-26 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.071, 108.071, 186.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Antibody 4E10 Fab light chain


Mass: 23395.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody 4E10 Fab Heavy chain


Mass: 24180.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.96 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: Sitting drops contain 4E10 Fab at 10 mg/ml, 10 mM Phosphatidylcholine (06:0 PC) sample mixed (1:1 v/v) with a reservoir solution of 0.2 M di-sodium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111), non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→46.781 Å / Num. obs: 12759 / % possible obs: 92.1 % / Redundancy: 8.6 % / Biso Wilson estimate: 75.4 Å2 / Rsym value: 0.085 / Net I/σ(I): 16
Reflection shellResolution: 2.81→2.86 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 5.3 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000HKL-2000 version 705bdata reduction
HKL-2000HKL-2000 version 705bdata scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FX7

2fx7


Resolution: 2.81→46.781 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 638 5 %Random selection
Rwork0.2214 ---
obs0.2239 12757 92.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.3 Å2
Refinement stepCycle: LAST / Resolution: 2.81→46.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 6 28 3262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033339
X-RAY DIFFRACTIONf_angle_d0.6374559
X-RAY DIFFRACTIONf_dihedral_angle_d13.131162
X-RAY DIFFRACTIONf_chiral_restr0.024524
X-RAY DIFFRACTIONf_plane_restr0.004591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-3.0260.38221270.31352419X-RAY DIFFRACTION94
3.026-3.33050.37761270.29762410X-RAY DIFFRACTION94
3.3305-3.81220.27221280.24042425X-RAY DIFFRACTION93
3.8122-4.80220.22741270.20042410X-RAY DIFFRACTION92
4.8022-46.78780.2611290.19252455X-RAY DIFFRACTION88

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