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- PDB-5bzd: Crystal Structure of PCDN-27A, an antibody from the PCDN family o... -

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Basic information

Entry
Database: PDB / ID: 5bzd
TitleCrystal Structure of PCDN-27A, an antibody from the PCDN family of HIV-1 antibodies
Components
  • 5G8 HIV Antibody heavy chain
  • 5G8 HIV Antibody light chain
KeywordsIMMUNE SYSTEM / HIV / Antibody / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGarces, F. / WILSON, I.A.
CitationJournal: Immunity / Year: 2016
Title: Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch
Authors: MacLead, D. / Choi, N.M. / Briney, B. / Garces, F. / Ver, L.S. / Landais, E. / Murrell, B. / Wrin, T. / Kilembe, W. / Liang, C.-H. / Ramos, A. / Bian, C. / Wickramasinghe, L. / Kong, L. / ...Authors: MacLead, D. / Choi, N.M. / Briney, B. / Garces, F. / Ver, L.S. / Landais, E. / Murrell, B. / Wrin, T. / Kilembe, W. / Liang, C.-H. / Ramos, A. / Bian, C. / Wickramasinghe, L. / Kong, L. / Eren, K. / Wu, C.-Y. / Wong, C.-H. / The IAVI Protocol C Investigators & The IAVI African HIV Research Network / Pond, S.L.K. / Wilson, I.A. / Burton, D.R. / Poignard, P.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
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 20, 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
A: 5G8 HIV Antibody light chain
B: 5G8 HIV Antibody heavy chain
C: 5G8 HIV Antibody light chain
D: 5G8 HIV Antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5805
Polymers96,4884
Non-polymers921
Water21612
1
A: 5G8 HIV Antibody light chain
B: 5G8 HIV Antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3363
Polymers48,2442
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-22 kcal/mol
Surface area20390 Å2
MethodPISA
2
C: 5G8 HIV Antibody light chain
D: 5G8 HIV Antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)48,2442
Polymers48,2442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-25 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.861, 120.375, 111.098
Angle α, β, γ (deg.)90.00, 96.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 5G8 HIV Antibody light chain


Mass: 23350.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): Human / Production host: Homo sapiens (human)
#2: Antibody 5G8 HIV Antibody heavy chain


Mass: 24892.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): Human / 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.: 12 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 16% (w/v) PEG 8000, 20% (v/v) glycerol and 0.04 M potassium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28257 / % possible obs: 93.9 % / Redundancy: 2.7 % / Rsym value: 0.12 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.73 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRH

1rrh


Resolution: 2.7→40.681 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1420 5.04 %
Rwork0.2107 --
obs0.2125 28177 93.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→40.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6709 0 6 12 6727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056894
X-RAY DIFFRACTIONf_angle_d0.9269375
X-RAY DIFFRACTIONf_dihedral_angle_d13.0112458
X-RAY DIFFRACTIONf_chiral_restr0.0411051
X-RAY DIFFRACTIONf_plane_restr0.0061202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79640.37311330.34632750X-RAY DIFFRACTION94
2.7964-2.90830.37421240.32372687X-RAY DIFFRACTION95
2.9083-3.04060.3641360.3072668X-RAY DIFFRACTION93
3.0406-3.20090.39261430.27932524X-RAY DIFFRACTION89
3.2009-3.40130.29031330.25062759X-RAY DIFFRACTION97
3.4013-3.66380.29731740.23362724X-RAY DIFFRACTION96
3.6638-4.03220.26151230.21352647X-RAY DIFFRACTION92
4.0322-4.6150.19241520.16392635X-RAY DIFFRACTION92
4.615-5.81170.17711380.16362746X-RAY DIFFRACTION96
5.8117-40.6860.20111640.17432617X-RAY DIFFRACTION91

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