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

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Basic information

Entry
Database: PDB / ID: 4xce
TitleCrystal structure of human 4E10 Fab crystalized in the presence of Phosphatidylcholine (06:0 PC); C2 space group
Components
  • 4E10 Fab heavy chain
  • 4E10 Fab light chain
KeywordsIMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 / Phosphatidylcholine / membrane lipid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 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 1.4Nov 6, 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
B: 4E10 Fab light chain
A: 4E10 Fab heavy chain
D: 4E10 Fab light chain
C: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)142,7286
Polymers142,7286
Non-polymers00
Water86548
1
L: 4E10 Fab light chain
H: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5762
Polymers47,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-26 kcal/mol
Surface area20250 Å2
MethodPISA
2
B: 4E10 Fab light chain
A: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5762
Polymers47,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-25 kcal/mol
Surface area19960 Å2
MethodPISA
3
D: 4E10 Fab light chain
C: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5762
Polymers47,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-25 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.524, 164.309, 106.990
Angle α, β, γ (deg.)90.00, 106.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 4E10 Fab light chain


Mass: 23395.850 Da / Num. of mol.: 3
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.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.94 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Sitting drops contain 4E10 Fab at 10 mg/ml, 10 mM Phosphatidylcholine (06:0 PC) sample mixed (1:1 v/v) with reservoir solution of 0.2 M potassium sodium tartrate, 20% PEG3350

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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: 2.93→46.995 Å / Num. obs: 31840 / % possible obs: 94.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 63.2 Å2 / Rsym value: 0.089 / Net I/σ(I): 9
Reflection shellResolution: 2.93→2.98 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.2 / % possible all: 95.7

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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: 2.93→46.995 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1591 5 %Random selection
Rwork0.1918 ---
obs0.1946 31822 93.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.7 Å2
Refinement stepCycle: LAST / Resolution: 2.93→46.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9616 0 0 48 9664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049917
X-RAY DIFFRACTIONf_angle_d0.91313542
X-RAY DIFFRACTIONf_dihedral_angle_d13.4923448
X-RAY DIFFRACTIONf_chiral_restr0.0341563
X-RAY DIFFRACTIONf_plane_restr0.0051758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.02090.4111340.3142553X-RAY DIFFRACTION87
3.0209-3.12890.28611490.25562821X-RAY DIFFRACTION97
3.1289-3.25410.32871490.25142820X-RAY DIFFRACTION96
3.2541-3.40220.29641470.23172805X-RAY DIFFRACTION95
3.4022-3.58150.28891400.20072670X-RAY DIFFRACTION92
3.5815-3.80580.27971470.19692811X-RAY DIFFRACTION95
3.8058-4.09950.25111470.18682780X-RAY DIFFRACTION95
4.0995-4.51180.23391470.15582800X-RAY DIFFRACTION95
4.5118-5.16390.20341440.15092731X-RAY DIFFRACTION93
5.1639-6.50320.20181460.18982763X-RAY DIFFRACTION94
6.5032-47.0010.20841410.1782677X-RAY DIFFRACTION89

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