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- PDB-5ifh: Crystal structure of the BCR Fab fragment from subset #2 case P11475 -

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Basic information

Entry
Database: PDB / ID: 5ifh
TitleCrystal structure of the BCR Fab fragment from subset #2 case P11475
Components
  • Heavy chain of the Fab fragment from BCR derived from the P11475 CLL clone
  • Light chain of the Fab fragment from BCR derived from the P11475 CLL clone
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / B cell receptor / chronic lymphocytic leukemia
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å
AuthorsMinici, C. / Degano, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
AIRCIG 17032 Italy
CitationJournal: Nat Commun / Year: 2017
Title: Distinct homotypic B-cell receptor interactions shape the outcome of chronic lymphocytic leukaemia.
Authors: Minici, C. / Gounari, M. / Ubelhart, R. / Scarfo, L. / Duhren-von Minden, M. / Schneider, D. / Tasdogan, A. / Alkhatib, A. / Agathangelidis, A. / Ntoufa, S. / Chiorazzi, N. / Jumaa, H. / ...Authors: Minici, C. / Gounari, M. / Ubelhart, R. / Scarfo, L. / Duhren-von Minden, M. / Schneider, D. / Tasdogan, A. / Alkhatib, A. / Agathangelidis, A. / Ntoufa, S. / Chiorazzi, N. / Jumaa, H. / Stamatopoulos, K. / Ghia, P. / Degano, M.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of the Fab fragment from BCR derived from the P11475 CLL clone
L: Light chain of the Fab fragment from BCR derived from the P11475 CLL clone


Theoretical massNumber of molelcules
Total (without water)46,9762
Polymers46,9762
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.872, 65.872, 111.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody Heavy chain of the Fab fragment from BCR derived from the P11475 CLL clone


Mass: 23883.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain of the Fab fragment from BCR derived from the P11475 CLL clone


Mass: 23092.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M BisTris pH 5.5, 200 mM MgCl2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97241 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2015
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97241 Å / Relative weight: 1
ReflectionResolution: 2.29→65.87 Å / Num. obs: 21207 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 40.2 Å2 / CC1/2: 0.998 / Rsym value: 0.119 / Net I/av σ(I): 4.8 / Net I/σ(I): 121.7
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.84 / Mean I/σ(I) obs: 2.9 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ADQ

1adq


Resolution: 2.293→65.87 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.44
Details: X-ray target function: twin_lsq_f Twinning operator h, -k, -l Refined twinning fraction: 0.28
RfactorNum. reflection% reflection
Rfree0.2089 1078 5.13 %
Rwork0.1797 --
obs0.183 21028 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.1884 Å20 Å20 Å2
2--2.1884 Å20 Å2
3----8.919 Å2
Refinement stepCycle: LAST / Resolution: 2.293→65.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 0 70 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023033
X-RAY DIFFRACTIONf_angle_d0.7464127
X-RAY DIFFRACTIONf_dihedral_angle_d11.7981078
X-RAY DIFFRACTIONf_chiral_restr0.045457
X-RAY DIFFRACTIONf_plane_restr0.003532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.297-2.40150.35421170.30632397X-RAY DIFFRACTION91
2.4015-2.52810.31551280.26692491X-RAY DIFFRACTION94
2.5281-2.68650.27091180.24532488X-RAY DIFFRACTION95
2.6865-2.8940.26011570.20152475X-RAY DIFFRACTION94
2.894-3.18520.22691210.18192514X-RAY DIFFRACTION95
3.1852-3.64610.21051600.17742493X-RAY DIFFRACTION94
3.6461-4.59350.16211060.14912538X-RAY DIFFRACTION96
4.5935-65.89910.20691670.15762530X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.09382.23830.67627.91452.34472.41540.3575-0.36660.72950.8087-0.56521.562-0.1315-0.33810.20260.61840.0360.22670.4404-0.02530.560974.403655.57029.1882
24.8563-3.70722.67765.56460.97776.45060.077-0.7758-0.14090.72990.1590.046-0.0172-0.4036-0.20060.5236-0.05160.07760.2788-0.0380.298883.509149.255310.9359
32.55333.3478-0.4255.67720.14925.14820.3306-1.60050.49931.13-0.27440.1875-0.0047-0.0074-0.1330.92130.02110.17120.5128-0.04890.427583.407153.271117.5261
48.18792.25065.98127.45412.93438.6745-0.1046-1.48190.58290.8125-0.17371.71350.2375-1.04920.30310.7225-0.040.35580.5401-0.12090.73572.443754.616514.3565
54.66791.39131.40057.3452.52456.8121-0.0379-0.36720.0440.37660.150.0633-0.0482-0.1721-0.11420.5026-0.00650.13670.2773-0.01190.31282.656152.63196.674
64.05730.44951.80640.3872-0.5392.8330.5793-0.09211.18720.3998-0.3240.1639-0.03990.0367-0.23150.7854-0.01380.18110.343-0.17310.735584.609372.14866.3014
75.3012-3.14782.89295.8937-5.49225.4214-0.49360.19010.3175-0.86250.08191.181-0.7091-0.28870.27260.91010.0512-0.27360.35950.06820.715181.594379.4981-8.3537
82.0190.82152.41163.62491.34878.0373-0.71390.1410.1092-0.7871-0.10561.56790.3229-0.96130.78861.0787-0.2021-0.2990.36610.00361.000478.95772.3058-11.7404
94.22810.24440.2977.4029-2.09559.71720.2666-0.24870.6499-0.54180.13270.788-0.2755-0.0592-0.27710.44120.03150.03570.36470.00460.613188.074576.3281-5.0544
103.63790.2242.35381.61980.87771.86450.2286-1.1934-0.0762-0.5677-0.45811.83520.3494-1.29190.11450.7008-0.2314-0.32030.9385-0.01071.766173.779978.5459-8.2878
113.24740.2717-0.59033.6211-1.41795.71510.1325-0.0670.09330.3358-0.01420.00720.0487-0.0403-0.09210.3266-0.02190.00420.1318-0.02340.289889.628242.0284-5.8874
120.42910.29080.29115.64590.52890.1789-0.11910.0725-0.1362-1.32280.2636-0.2969-0.93960.4895-0.07871.1124-0.22960.06340.2974-0.06780.590693.10577.4731-18.838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 60 )
3X-RAY DIFFRACTION3chain 'H' and (resid 61 through 73 )
4X-RAY DIFFRACTION4chain 'H' and (resid 74 through 83 )
5X-RAY DIFFRACTION5chain 'H' and (resid 84 through 109 )
6X-RAY DIFFRACTION6chain 'H' and (resid 110 through 122 )
7X-RAY DIFFRACTION7chain 'H' and (resid 123 through 154 )
8X-RAY DIFFRACTION8chain 'H' and (resid 155 through 174 )
9X-RAY DIFFRACTION9chain 'H' and (resid 175 through 185 )
10X-RAY DIFFRACTION10chain 'H' and (resid 186 through 218 )
11X-RAY DIFFRACTION11chain 'L' and (resid 2 through 109 )
12X-RAY DIFFRACTION12chain 'L' and (resid 110 through 212 )

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