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- PDB-2xxc: Crystal structure of a camelid VHH raised against the HIV-1 capsi... -

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Basic information

Entry
Database: PDB / ID: 2xxc
TitleCrystal structure of a camelid VHH raised against the HIV-1 capsid protein C-terminal domain.
ComponentsCAMELID VHH 9
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesVICUGNA PACOS (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsIgonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A.
CitationJournal: To be Published
Title: Targeting HIV-1 Virion Formation with Nanobodies -Implications for the Design of Assembly Inhibitors
Authors: Igonet, S. / Vaney, M.C. / Bartonova, V. / Helma, J. / Rothbauer, U. / Leonhardt, H. / Stura, E. / Krausslich, H.-G. / Rey, F.A.
History
DepositionNov 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CAMELID VHH 9


Theoretical massNumber of molelcules
Total (without water)13,2141
Polymers13,2141
Non-polymers00
Water2,792155
1
B: CAMELID VHH 9

B: CAMELID VHH 9


Theoretical massNumber of molelcules
Total (without water)26,4282
Polymers26,4282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1710 Å2
ΔGint-5.5 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.208, 80.208, 52.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody CAMELID VHH 9


Mass: 13213.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VICUGNA PACOS (alpaca) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE VHH RESIDUES (CHAIN B) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. THE 6XHISTIDINE TAG AT ...THE VHH RESIDUES (CHAIN B) ARE NUMBERED ACCORDING TO THE KABAT NUMBERING. THE 6XHISTIDINE TAG AT THE C-TERMINUS IS DISORDERED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.72 % / Description: NONE
Crystal growDetails: 28-30 % W/V PEG 4000, 100 MM SODIUM CITRATE PH 4.6, 100 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2009
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.67→32 Å / Num. obs: 19028 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 25.32 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.5
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 58.3

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XT1

2xt1


Resolution: 1.67→13.19 Å / Cor.coef. Fo:Fc: 0.9447 / Cor.coef. Fo:Fc free: 0.9249 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.085
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. THE 6XHISTIDINE TAG AT THE C-TERMINUS IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 958 5.06 %RANDOM
Rwork0.18 ---
obs0.1815 18940 92.64 %-
Displacement parametersBiso mean: 30.26 Å2
Baniso -1Baniso -2Baniso -3
1-5.1261 Å20 Å20 Å2
2--5.1261 Å20 Å2
3----10.2522 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.67→13.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 0 155 1010
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01944HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.151282HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d348SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes149HARMONIC5
X-RAY DIFFRACTIONt_it944HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion16.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion119SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1205SEMIHARMONIC4
LS refinement shellResolution: 1.67→1.76 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2749 94 5.98 %
Rwork0.2517 1477 -
all0.2531 1571 -
obs--92.64 %

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