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

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Basic information

Entry
Database: PDB / ID: 4xbp
TitleCrystal structure of human 4E10 Fab crystalized in the presence of Phosphatidylethanolamine (06:0 PE)
Components
  • 4E10 FAB LIGHT CHAIN
  • 4E10 Fab heavy chain
KeywordsIMMUNE SYSTEM / human 4E10 Fab anti HIV-1 gp41 / membrane lipids / Phosphatidylethanolamine
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 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

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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
F: 4E10 FAB LIGHT CHAIN
E: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,3969
Polymers190,3048
Non-polymers921
Water1,802100
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 area3140 Å2
ΔGint-24 kcal/mol
Surface area19600 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 area3140 Å2
ΔGint-23 kcal/mol
Surface area19460 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 area3000 Å2
ΔGint-23 kcal/mol
Surface area19150 Å2
MethodPISA
4
F: 4E10 FAB LIGHT CHAIN
E: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6683
Polymers47,5762
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-24 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.426, 111.744, 146.196
Angle α, β, γ (deg.)90.00, 93.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
4E10 FAB LIGHT CHAIN


Mass: 23395.850 Da / Num. of mol.: 4
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.: 4
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.: 100 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: Sitting drops contain 4E10 Fab at 10 mg/ml, 10 mM Phosphatidylethanolamine (06:0 PE) sample stock mixed (1:1 ratio) with reservoir solution of 20% PEG 6000, 0.1M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03323 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 2.94→49.159 Å / Num. obs: 33714 / % possible obs: 92.7 % / Redundancy: 4 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.178 / Net I/σ(I): 6.5
Reflection shellResolution: 2.94→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.9 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FX7

2fx7


Resolution: 2.94→49.159 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 1688 5.02 %Random selection
Rwork0.228 ---
obs0.2303 33632 91.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 2.94→49.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12858 0 6 100 12964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313236
X-RAY DIFFRACTIONf_angle_d0.73718059
X-RAY DIFFRACTIONf_dihedral_angle_d12.794619
X-RAY DIFFRACTIONf_chiral_restr0.0282080
X-RAY DIFFRACTIONf_plane_restr0.0042344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.02570.40321340.32562475X-RAY DIFFRACTION86
3.0257-3.12340.34851360.30072747X-RAY DIFFRACTION95
3.1234-3.2350.31441540.27922693X-RAY DIFFRACTION94
3.235-3.36450.31121420.27052729X-RAY DIFFRACTION94
3.3645-3.51760.33241450.25552720X-RAY DIFFRACTION94
3.5176-3.7030.28631410.24012660X-RAY DIFFRACTION93
3.703-3.93490.30711460.22952683X-RAY DIFFRACTION93
3.9349-4.23850.25911410.21112700X-RAY DIFFRACTION93
4.2385-4.66480.20181280.17972666X-RAY DIFFRACTION92
4.6648-5.33910.23791460.18172670X-RAY DIFFRACTION91
5.3391-6.7240.22811410.20452629X-RAY DIFFRACTION90
6.724-49.16610.20021340.19612572X-RAY DIFFRACTION87

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