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- PDB-4fq1: Crystal Structure of PGT121 Fab -

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Basic information

Entry
Database: PDB / ID: 4fq1
TitleCrystal Structure of PGT121 Fab
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / IG FOLD / ANTI HIV / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsScharf, L. / Bjorkman, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies.
Authors: Mouquet, H. / Scharf, L. / Euler, Z. / Liu, Y. / Eden, C. / Scheid, J.F. / Halper-Stromberg, A. / Gnanapragasam, P.N. / Spencer, D.I. / Seaman, M.S. / Schuitemaker, H. / Feizi, T. / ...Authors: Mouquet, H. / Scharf, L. / Euler, Z. / Liu, Y. / Eden, C. / Scheid, J.F. / Halper-Stromberg, A. / Gnanapragasam, P.N. / Spencer, D.I. / Seaman, M.S. / Schuitemaker, H. / Feizi, T. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionJun 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 19, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,1683
Polymers48,9462
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-22 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.753, 74.672, 114.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab heavy chain


Mass: 26343.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 22602.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: homo sapiens (human)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 50.55 %
Crystal growTemperature: 298 K / pH: 8.5
Details: PEG 4000, Tris HCl, CuCl2, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2011
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.776→38.306 Å / Num. obs: 12460 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.099 / Net I/σ(I): 8.8
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.293 / % possible all: 84.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.78 Å35.52 Å
Translation2.78 Å35.52 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→35.51 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 504 5 %
Rwork0.216 --
obs0.218 10076 98.27 %
all-12552 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2.172 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.9498 Å20 Å2-0 Å2
2--8.6192 Å20 Å2
3----6.6694 Å2
Refinement stepCycle: LAST / Resolution: 3→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 15 0 3307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053397
X-RAY DIFFRACTIONf_angle_d0.9714633
X-RAY DIFFRACTIONf_dihedral_angle_d13.4041201
X-RAY DIFFRACTIONf_chiral_restr0.063525
X-RAY DIFFRACTIONf_plane_restr0.003588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0004-3.30210.29631230.25752349X-RAY DIFFRACTION99
3.3021-3.77950.29691260.22532386X-RAY DIFFRACTION99
3.7795-4.75990.22311250.18232373X-RAY DIFFRACTION98
4.7599-35.51140.25951300.21412464X-RAY DIFFRACTION97

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