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- PDB-5drw: Crystal structure of the BCR Fab fragment from subset #4 case CLL183 -

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Basic information

Entry
Database: PDB / ID: 5drw
TitleCrystal structure of the BCR Fab fragment from subset #4 case CLL183
Components
  • CLL183 BCR antibody heavy chain
  • CLL183 BCR antibody light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / B-cell receptor / chronic lymphocytic leukemia / Receptor-ligand complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
Model detailsAutologous recognition by CLL-derived BCRs
AuthorsMinici, C. / Degano, M.
Funding support Italy, 2items
OrganizationGrant numberCountry
AIRC5xMille Italy
Fondazione Intesa San Paolo Onlus 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
DepositionSep 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLL183 BCR antibody heavy chain
B: CLL183 BCR antibody light chain


Theoretical massNumber of molelcules
Total (without water)48,3062
Polymers48,3062
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-22 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.210, 90.210, 131.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody CLL183 BCR antibody heavy chain


Mass: 24249.070 Da / Num. of mol.: 1
Fragment: Heavy chain variable (VH) and constant (CH1) domains
Source method: isolated from a genetically manipulated source
Details: Chronic lymphocytic leukemia clone / Source: (gene. exp.) Homo sapiens (human) / Cell: B lymphocyte / Gene: IGHV4-34, IGHJ6, IGHG1*03 / Production host: Escherichia coli (E. coli)
#2: Antibody CLL183 BCR antibody light chain


Mass: 24056.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chronic lymphocytic leukemia clone / Source: (gene. exp.) Homo sapiens (human) / Cell: B lymphocyte / Gene: IGKV2-30, IGKJ2, IGKC*01 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M NaCitrate, 0.1 M ammonium sulfate, 1% hexanediol, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2013
RadiationMonochromator: SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.27→42.66 Å / Num. obs: 25817 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.113 / Net I/av σ(I): 5.1 / Net I/σ(I): 10.7
Reflection shellResolution: 2.27→2.34 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
Aimlessdata scaling
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DN0

1dn0


Resolution: 2.27→42.66 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1319 5.12 %Random selection
Rwork0.195 24447 --
obs0.1973 25766 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.63 Å2 / Biso mean: 59.6517 Å2 / Biso min: 25.27 Å2
Refinement stepCycle: final / Resolution: 2.27→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 90 3442
Biso mean---46.7 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073440
X-RAY DIFFRACTIONf_angle_d1.0364683
X-RAY DIFFRACTIONf_chiral_restr0.067525
X-RAY DIFFRACTIONf_plane_restr0.005597
X-RAY DIFFRACTIONf_dihedral_angle_d12.9761228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.268-2.35880.331330.283726562789
2.3588-2.46610.29571690.253226392808
2.4661-2.59610.26481390.236726742813
2.5961-2.75880.29811340.232126932827
2.7588-2.97170.30091460.236626892835
2.9717-3.27070.30021570.218926882845
3.2707-3.74370.24251360.20927292865
3.7437-4.71570.19181550.154727652920
4.7157-42.66310.20491500.161529143064
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)
19.35396.9807-5.69456.0597-5.88416.52490.696-0.92470.10761.09-0.6624-0.7348-0.9114-0.12380.10390.44960.07340.04710.3572-0.00460.45848.276834.11229.4725
23.63212.45060.6866.388-1.4931.04830.10970.11440.53470.1621-0.02920.2566-0.3132-0.193-0.04920.3890.09190.06830.39260.02630.29645.506131.538822.5597
33.6713-0.9084-0.15015.22791.04273.8318-0.39270.20010.2267-0.18370.263-0.326-0.1255-0.5338-0.1130.33610.00670.07950.35090.07790.4019.201926.413716.8748
42.80991.6704-1.18161.5643-1.07052.3258-0.13930.17570.1974-0.02560.1920.1698-0.1378-0.32-0.05630.34290.04790.00250.36720.06730.30098.438529.285419.4044
53.5424-0.9819-0.8082.5596-0.04523.0048-0.3877-1.2655-1.07670.51590.1021-0.2580.32990.61690.01980.53460.15530.02980.77850.31280.466812.21999.196451.103
64.2471-0.53914.6760.0777-0.62025.2009-0.8327-2.1628-0.50330.60130.2887-0.04790.30380.4310.13470.6860.29520.08971.01740.32430.36675.39412.503555.7028
79.41530.80923.79652.39770.41755.3923-0.2228-0.5852-1.13890.26630.1162-0.05690.30750.36080.00840.43190.15690.15370.40990.13890.565230.723215.987421.7572
83.43660.1525-1.93743.1297-1.61734.8068-0.14360.043-0.1345-0.2478-0.1879-0.2801-0.04010.50910.35190.304-0.05370.09570.27980.03670.322825.396827.832516.9256
93.1373-1.4741.32362.3822-0.0123.8419-0.38490.05230.0168-0.03130.2757-0.5223-0.1030.66660.06650.3701-0.01050.08810.50340.11220.473834.093725.945419.6797
108.1691-0.46454.77811.501-0.76663.351-0.4202-0.5424-0.56980.02930.3181-0.1591-0.85740.26180.08860.47460.02730.1510.43690.08950.400826.355323.84122.4892
115.1579-2.5574.87023.4509-3.30164.9467-0.22390.29230.0033-0.1671-0.2908-0.43250.7570.45250.28040.51580.10570.14990.39130.0550.506622.253718.589621.6084
128.17140.3728-2.23013.4403-1.50013.7522-0.5866-0.5854-2.22530.1519-0.28430.48720.91260.5530.64160.6660.21120.19440.6320.28241.045419.85860.818345.7296
135.53571.10010.70670.29770.76854.85830.61990.32560.2561-0.3618-0.68090.25860.66850.2870.08060.9917-0.05750.2680.6103-0.07191.198415.1488-9.540939.2437
145.95663.1246-0.68088.3081-1.95477.5189-0.76720.5066-0.27970.50660.60070.0711-0.17640.66860.17120.37450.13330.07590.53960.14790.586124.566310.058241.8637
155.54211.8168-1.86071.1503-2.26365.60730.18350.54530.38841.11780.0471.89620.9406-1.2333-0.38821.0431-0.20120.28650.54470.12771.83136.531-10.838245.7869
163.34650.69850.67260.28990.54051.18530.3964-0.0227-1.0515-0.1485-0.7714-1.21190.27330.06830.36061.1220.30990.46710.52290.22331.621423.8032-8.310145.4203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:11)A1 - 11
2X-RAY DIFFRACTION2(chain A and resid 12:38)A12 - 38
3X-RAY DIFFRACTION3(chain A and resid 39:58)A39 - 58
4X-RAY DIFFRACTION4(chain A and resid 59:127)A59 - 127
5X-RAY DIFFRACTION5(chain A and resid 128:208)A128 - 208
6X-RAY DIFFRACTION6(chain A and resid 209:226)A209 - 226
7X-RAY DIFFRACTION7(chain B and resid 1:24)B1 - 24
8X-RAY DIFFRACTION8(chain B and resid 25:60)B25 - 60
9X-RAY DIFFRACTION9(chain B and resid 61:81)B61 - 81
10X-RAY DIFFRACTION10(chain B and resid 82:99)B82 - 99
11X-RAY DIFFRACTION11(chain B and resid 100:112)B100 - 112
12X-RAY DIFFRACTION12(chain B and resid 113:151)B113 - 151
13X-RAY DIFFRACTION13(chain B and resid 152:166)B152 - 166
14X-RAY DIFFRACTION14(chain B and resid 167:183)B167 - 183
15X-RAY DIFFRACTION15(chain B and resid 184:196)B184 - 196
16X-RAY DIFFRACTION16(chain B and resid 197:217)B197 - 217

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