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- PDB-1rhh: Crystal Structure of the Broadly HIV-1 Neutralizing Fab X5 at 1.9... -

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Basic information

Entry
Database: PDB / ID: 1rhh
TitleCrystal Structure of the Broadly HIV-1 Neutralizing Fab X5 at 1.90 Angstrom Resolution
Components
  • Fab X5, heavy chain
  • Fab X5, light chain
KeywordsIMMUNE SYSTEM / Fab / antibody / X5 / HIV-1 / Broadly Neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDarbha, R. / Phogat, S. / Labrijn, A.F. / Shu, Y. / Gu, Y. / Andrykovitch, M. / Zhang, M.Y. / Pantophlet, R. / Martin, L. / Vita, C. ...Darbha, R. / Phogat, S. / Labrijn, A.F. / Shu, Y. / Gu, Y. / Andrykovitch, M. / Zhang, M.Y. / Pantophlet, R. / Martin, L. / Vita, C. / Burton, D.R. / Dimitrov, D.S. / Ji, X.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of the Broadly Cross-Reactive HIV-1-Neutralizing Fab X5 and Fine Mapping of Its Epitope
Authors: Darbha, R. / Phogat, S. / Labrijn, A.F. / Shu, Y. / Gu, Y. / Andrykovitch, M. / Zhang, M.Y. / Pantophlet, R. / Martin, L. / Vita, C. / Burton, D.R. / Dimitrov, D.S. / Ji, X.
History
DepositionNov 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab X5, light chain
B: Fab X5, heavy chain
C: Fab X5, light chain
D: Fab X5, heavy chain


Theoretical massNumber of molelcules
Total (without water)97,3824
Polymers97,3824
Non-polymers00
Water11,151619
1
A: Fab X5, light chain
B: Fab X5, heavy chain


Theoretical massNumber of molelcules
Total (without water)48,6912
Polymers48,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-29 kcal/mol
Surface area20120 Å2
MethodPISA
2
C: Fab X5, light chain
D: Fab X5, heavy chain


Theoretical massNumber of molelcules
Total (without water)48,6912
Polymers48,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-27 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.600, 139.600, 120.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological unit consists of a light chain and a heavy chain. The biological unit is half of the asymmetric unit

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Components

#1: Antibody Fab X5, light chain


Mass: 23267.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q6GMV9
#2: Antibody Fab X5, heavy chain


Mass: 25423.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q6PJF1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG400, HEPES, 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 17-19 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1droppH7.4
210 mg/mlprotein1drop
330 %1,2-propanediol1reservoir
420 %PEG4001reservoir
50.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2001 / Details: Mirror
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.9→29.41 Å / Num. all: 93650 / Num. obs: 93615 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 39.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.0498 / Mean I/σ(I) obs: 3.2 / Num. unique all: 9208 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % possible obs: 100 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.498

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FCT

3fct


Resolution: 1.9→29.41 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5551019.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4699 5 %RANDOM
Rwork0.224 ---
obs0.224 93615 99.8 %-
all-93615 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2943 Å2 / ksol: 0.343409 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å20 Å20 Å2
2--5.21 Å20 Å2
3----10.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-30 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6747 0 0 619 7366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 767 5 %
Rwork0.27 14575 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.29

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