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- PDB-2xa3: crystal structure of the broadly neutralizing llama VHH D7 and it... -

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Basic information

Entry
Database: PDB / ID: 2xa3
Titlecrystal structure of the broadly neutralizing llama VHH D7 and its mode of HIV-1 gp120 interaction
ComponentsLLAMA HEAVY CHAIN ANTIBODY D7
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHinz, A. / Lutje Hulsik, D. / Forsman, A. / Koh, W. / Belrhali, H. / Gorlani, A. / de Haard, H. / Weiss, R.A. / Verrips, T. / Weissenhorn, W.
Citation
Journal: PLoS ONE / Year: 2010
Title: Crystal structure of the neutralizing Llama V(HH) D7 and its mode of HIV-1 gp120 interaction.
Authors: Hinz, A. / Lutje Hulsik, D. / Forsman, A. / Koh, W.W. / Belrhali, H. / Gorlani, A. / de Haard, H. / Weiss, R.A. / Verrips, T. / Weissenhorn, W.
#1: Journal: J.Virol. / Year: 2008
Title: Llama Antibody Fragments with Cross-Subtype Human Immunodeficiency Virus Type 1 (HIV-1)-Neutralizing Properties and High Affinity for HIV-1 Gp120.
Authors: Forsman, A. / Beirnaert, E. / Aasa-Chapman, M.M.I. / Hoorelbeke, B. / Hijazi, K. / Koh, W. / Tack, V. / Szynol, A. / Kelly, C. / Mcknight, A. / Verrips, T. / De Haard, H. / Weiss, R.A.
History
DepositionMar 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LLAMA HEAVY CHAIN ANTIBODY D7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2845
Polymers13,8991
Non-polymers3844
Water3,099172
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.370, 62.180, 62.740
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 LLAMA HEAVY CHAIN ANTIBODY D7


Mass: 13899.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VARIABLE DOMAIN OF A HEAVY CHAIN ANTIBODY / Source: (gene. exp.) LAMA GLAMA (llama) / Tissue: BLOOD / Cell: LYMPHOCYTE / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Variant (production host): VWK18GAL1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATIONS DONE V5Q, A11V, G24A, A61V, A69D, S80Y.

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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: 2.87 Å3/Da / Density % sol: 57.2 % / Description: NONE
Crystal growpH: 6
Details: 5 MG/ML OF D7 PROTEIN IN A SOLUTION OF 20MM HEPES PH 7, 0.1 M NACL MIXED WITH AN EQUAL VOLUME OF 100MM SODIUM CACODYLATE PH 6, 20 MM MAGNESIUM ACETATE, 1.7M AMMONIUM SULFATE AND 19 % GLYCEROL WELL CONDITION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.974
DetectorType: MARRESEARCH / Date: Jul 20, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.5→44 Å / Num. obs: 22695 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 13.39 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellHighest resolution: 1.5 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.5 / % possible all: 68.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCV

1hcv


Resolution: 1.5→24.027 Å / SU ML: 0.17 / σ(F): 0.08 / Phase error: 15.88 / Stereochemistry target values: ML
Details: DISORDERED REGIONS FOR THE CDR3 LOOP FROM RESIDUE 98 TO RESIDUE 100C.
RfactorNum. reflection% reflection
Rfree0.1935 1135 5.1 %
Rwork0.1657 --
obs0.167 22364 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.488 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2255 Å20 Å20 Å2
2---0.4192 Å20 Å2
3---1.6447 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 20 172 1169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061199
X-RAY DIFFRACTIONf_angle_d1.0651652
X-RAY DIFFRACTIONf_dihedral_angle_d16.816434
X-RAY DIFFRACTIONf_chiral_restr0.071167
X-RAY DIFFRACTIONf_plane_restr0.005225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.56840.2226940.18121816X-RAY DIFFRACTION65
1.5684-1.65110.19961250.16172311X-RAY DIFFRACTION82
1.6511-1.75450.19291490.16292737X-RAY DIFFRACTION98
1.7545-1.88990.20991620.16272788X-RAY DIFFRACTION99
1.8899-2.080.17651680.15582816X-RAY DIFFRACTION99
2.08-2.38070.17731470.15912836X-RAY DIFFRACTION100
2.3807-2.99850.22151500.16622881X-RAY DIFFRACTION100
2.9985-24.02980.16161400.16183044X-RAY DIFFRACTION100

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