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- PDB-6xsn: Crystal structure of NHP VD20.5A4 Fab in complex with 16055 V1V2 ... -

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Basic information

Entry
Database: PDB / ID: 6xsn
TitleCrystal structure of NHP VD20.5A4 Fab in complex with 16055 V1V2 1FD6 scaffold
Components
  • 16055_V1V2-1FD6
  • VD20.5A4_heavy_chain
  • VD20.5A4_light_chain
KeywordsIMMUNE SYSTEM / VD20.5A4 Fab / antibody / NHPs / Fab / 16055 V1V2 / 1FD6 scaffold
Function / homologyTHIOCYANATE ION
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsAljedani, S. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01 AI104722 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization.
Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / ...Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / O'Dell, S. / Mascola, J.R. / Lee, K.K. / Karlsson Hedestam, G.B. / Wyatt, R.T. / Pancera, M.
History
DepositionJul 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: VD20.5A4_heavy_chain
L: VD20.5A4_light_chain
C: 16055_V1V2-1FD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,53512
Polymers62,8683
Non-polymers6679
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.565, 106.565, 128.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody VD20.5A4_heavy_chain


Mass: 23837.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey)
#2: Antibody VD20.5A4_light_chain


Mass: 23171.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey)

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Protein / Sugars , 2 types, 2 molecules C

#3: Protein 16055_V1V2-1FD6


Mass: 15858.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey)
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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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Non-polymers , 4 types, 53 molecules

#4: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Na Acet 5.5 pH 10%w/v PEG 8K 10%w/v PEG 1K 0.2M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→106.6 Å / Num. obs: 17667 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 48.94 Å2 / CC1/2: 1 / Net I/σ(I): 10.88
Reflection shellResolution: 2.87→2.92 Å / Num. unique obs: 17702 / CC1/2: 0.98 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Coot1.17.1_3660model building
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U3Z

6u3z


Resolution: 2.87→49.24 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 817 4.93 %
Rwork0.2208 --
obs0.2231 16586 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3559 0 40 45 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033673
X-RAY DIFFRACTIONf_angle_d0.7655004
X-RAY DIFFRACTIONf_dihedral_angle_d21.8991264
X-RAY DIFFRACTIONf_chiral_restr0.047575
X-RAY DIFFRACTIONf_plane_restr0.005642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.050.29911000.2751767X-RAY DIFFRACTION65
3.05-3.280.38381300.27312695X-RAY DIFFRACTION98
3.28-3.610.31621580.2432737X-RAY DIFFRACTION100
3.61-4.130.27471230.222789X-RAY DIFFRACTION100
4.13-5.210.19541320.17152828X-RAY DIFFRACTION100
5.21-49.240.24651740.22142953X-RAY DIFFRACTION100

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