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- PDB-3ntc: Crystal structure of KD-247 Fab, an anti-V3 antibody that inhibit... -

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Basic information

Entry
Database: PDB / ID: 3ntc
TitleCrystal structure of KD-247 Fab, an anti-V3 antibody that inhibits HIV-1 Entry
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / KD-247 / humanized antibody / anti-V3 / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSarafianos, S.G. / Kirby, K.A.
CitationJournal: Faseb J. / Year: 2015
Title: Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247.
Authors: Kirby, K.A. / Ong, Y.T. / Hachiya, A. / Laughlin, T.G. / Chiang, L.A. / Pan, Y. / Moran, J.L. / Marchand, B. / Singh, K. / Gallazzi, F. / Quinn, T.P. / Yoshimura, K. / Murakami, T. / ...Authors: Kirby, K.A. / Ong, Y.T. / Hachiya, A. / Laughlin, T.G. / Chiang, L.A. / Pan, Y. / Moran, J.L. / Marchand, B. / Singh, K. / Gallazzi, F. / Quinn, T.P. / Yoshimura, K. / Murakami, T. / Matsushita, S. / Sarafianos, S.G.
History
DepositionJul 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 19, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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

Downloads & links

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,55917
Polymers47,5632
Non-polymers99615
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-14 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.060, 69.180, 111.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab light chain


Mass: 24178.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus
Description: The source is engineered human constant and framework regions with CDRs from Mouse
Fragment: Homo sapiens, Mus musculus
#2: Antibody Fab heavy chain


Mass: 23384.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus
Description: The source is engineered human constant and framework regions with CDRs from Mouse
Fragment: Homo sapiens, Mus musculus

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Non-polymers , 4 types, 516 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 3.9
Details: Ammonium Sulfate, Sodium Acetate, pH 3.9, vapor diffusion, sitting drop, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→19.75 Å / Num. obs: 68504 / % possible obs: 88.4 % / Redundancy: 5.56 % / Rmerge(I) obs: 0.071 / Χ2: 0.96 / Net I/σ(I): 11 / Scaling rejects: 2576
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.55-1.615.020.4852.43015359950.8787.1
1.61-1.675.110.4312.73066459960.9288
1.67-1.755.260.3443.33151659840.9286.9
1.75-1.845.50.254.53211558290.9385.4
1.84-1.955.790.18463337257580.9283.3
1.95-2.15.770.1268.83350357970.9183.8
2.1-2.315.590.09411.63285958620.8884.9
2.31-2.655.610.08113.73469061670.8888.4
2.65-3.335.680.05819.43900068280.9197.5
3.33-19.756.110.05728.24552771351.3197.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.88 Å19.75 Å
Translation1.88 Å19.75 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T3F

1t3f


Resolution: 1.55→19.75 Å / Occupancy max: 1.5 / Occupancy min: 0.06 / SU ML: 0.26 / σ(F): 1.33 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2748 4.01 %
Rwork0.1819 --
obs0.1836 68478 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.082 Å2 / ksol: 0.417 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.432 Å20 Å2-0 Å2
2--5.2789 Å20 Å2
3----3.8468 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 62 501 3905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063607
X-RAY DIFFRACTIONf_angle_d1.1564907
X-RAY DIFFRACTIONf_dihedral_angle_d13.5731329
X-RAY DIFFRACTIONf_chiral_restr0.067543
X-RAY DIFFRACTIONf_plane_restr0.005626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57670.34531150.26022892X-RAY DIFFRACTION87
1.5767-1.60530.31391280.25193064X-RAY DIFFRACTION93
1.6053-1.63620.32431430.24453134X-RAY DIFFRACTION97
1.6362-1.66960.30761150.23833290X-RAY DIFFRACTION99
1.6696-1.70580.24711430.20843300X-RAY DIFFRACTION100
1.7058-1.74550.24481490.18013286X-RAY DIFFRACTION100
1.7455-1.78910.24581350.18123273X-RAY DIFFRACTION100
1.7891-1.83750.24551230.17073287X-RAY DIFFRACTION100
1.8375-1.89150.28851220.17883324X-RAY DIFFRACTION100
1.8915-1.95250.24421320.17753328X-RAY DIFFRACTION100
1.9525-2.02220.23021510.16373298X-RAY DIFFRACTION100
2.0222-2.10310.23881390.15223323X-RAY DIFFRACTION100
2.1031-2.19870.21421400.14673315X-RAY DIFFRACTION100
2.1987-2.31440.21041430.15423294X-RAY DIFFRACTION100
2.3144-2.45920.20861430.15473334X-RAY DIFFRACTION100
2.4592-2.64870.21221240.16653380X-RAY DIFFRACTION100
2.6487-2.91450.23581570.16813326X-RAY DIFFRACTION100
2.9145-3.33440.18531270.15943379X-RAY DIFFRACTION100
3.3344-4.19440.18121540.14733407X-RAY DIFFRACTION100
4.1944-19.7550.17661650.17553496X-RAY DIFFRACTION99

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