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- PDB-3juy: Crystal Structure of a 3B3 Variant, a Broadly Neutralizing HIV-1 ... -

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Basic information

Entry
Database: PDB / ID: 3juy
TitleCrystal Structure of a 3B3 Variant, a Broadly Neutralizing HIV-1 scFv Antibody
Components3B3 single chain variant HIV-1 antibody
KeywordsIMMUNE SYSTEM / HIV / envelope protein gp120 / broadly neutralizing antibody / 3B3 single chain variable fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsClark, K.R. / Walsh, S.T.
CitationJournal: Protein Sci. / Year: 2009
Title: Crystal structure of a 3B3 variant-A broadly neutralizing HIV-1 scFv antibody.
Authors: Clark, K.R. / Walsh, S.T.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3B3 single chain variant HIV-1 antibody
A: 3B3 single chain variant HIV-1 antibody
C: 3B3 single chain variant HIV-1 antibody
E: 3B3 single chain variant HIV-1 antibody
F: 3B3 single chain variant HIV-1 antibody
D: 3B3 single chain variant HIV-1 antibody


Theoretical massNumber of molelcules
Total (without water)168,3666
Polymers168,3666
Non-polymers00
Water4,954275
1
A: 3B3 single chain variant HIV-1 antibody


Theoretical massNumber of molelcules
Total (without water)28,0611
Polymers28,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3B3 single chain variant HIV-1 antibody


Theoretical massNumber of molelcules
Total (without water)28,0611
Polymers28,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3B3 single chain variant HIV-1 antibody


Theoretical massNumber of molelcules
Total (without water)28,0611
Polymers28,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3B3 single chain variant HIV-1 antibody


Theoretical massNumber of molelcules
Total (without water)28,0611
Polymers28,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 3B3 single chain variant HIV-1 antibody


Theoretical massNumber of molelcules
Total (without water)28,0611
Polymers28,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 3B3 single chain variant HIV-1 antibody


Theoretical massNumber of molelcules
Total (without water)28,0611
Polymers28,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.172, 115.130, 92.374
Angle α, β, γ (deg.)90.00, 111.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
3B3 single chain variant HIV-1 antibody


Mass: 28060.965 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Plasmid: custom alakaline phosphatase single sequence vector
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RP
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 292 K / Method: sitting drop / pH: 6
Details: 20% w/v PEG-8000, 0.1 M MES, 0.2 M calcium acetate, pH 6.0, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 61604 / % possible obs: 92.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.124 / Χ2: 1.029 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.591.50.41143541.03965.8
2.59-2.691.80.40550611.06576.4
2.69-2.8220.35158601.0488
2.82-2.962.40.27964351.03896.8
2.96-3.152.80.2265731.02899.2
3.15-3.3930.17266831.01799.8
3.39-3.733.10.12866341.02399.7
3.73-4.273.20.10166541.03899.6
4.27-5.383.10.07566451.01898.9
5.38-303.10.06967051.02898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.752 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.802 / SU ML: 2.5 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 5927 10.1 %
Rwork0.195 --
obs0.201 58690 87.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.863 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 83.37 Å2 / Biso mean: 24.64 Å2 / Biso min: 3.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.988 Å2-0 Å2-0.229 Å2
2---3.976 Å2-0 Å2
3---6.964 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11000 0 0 275 11275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911302
X-RAY DIFFRACTIONf_angle_d1.19215312
X-RAY DIFFRACTIONf_chiral_restr0.0781599
X-RAY DIFFRACTIONf_plane_restr0.0051981
X-RAY DIFFRACTIONf_dihedral_angle_d16.1133890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5280.3541060.295927103348
2.528-2.5580.3351290.2731148127756
2.558-2.5890.3451260.2731204133061
2.589-2.6220.3671250.2811250137562
2.622-2.6570.3631610.2851301146266
2.657-2.6930.3791750.2851420159572
2.693-2.7310.3461710.2581485165674
2.731-2.7720.4071710.2531527169878
2.772-2.8150.3221810.2491667184882
2.815-2.8620.3292000.2321737193787
2.862-2.9110.3031960.2231806200291
2.911-2.9640.3282190.2191879209893
2.964-3.0210.2742160.2071876209295
3.021-3.0820.2852290.2061899212896
3.082-3.1490.2622190.2081894211396
3.149-3.2220.2812400.211958219897
3.222-3.3030.2831910.2011982217397
3.303-3.3920.2732400.1871926216697
3.392-3.4920.2331850.1671997218298
3.492-3.6040.2222220.1641981220399
3.604-3.7330.2432050.171970217599
3.733-3.8820.222130.1591982219599
3.882-4.0580.1992540.1541973222799
4.058-4.2720.2092040.151985218999
4.272-4.5380.1882310.1321975220698
4.538-4.8870.1822430.1421997224099
4.887-5.3770.1982050.1411989219498
5.377-6.1490.2212220.1642005222799
6.149-7.7240.2432140.1842013222798
7.724-29.7540.2352340.2082010224498

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