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- PDB-5drx: Crystal structure of the BCR Fab fragment from subset #4 case CLL240 -

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Basic information

Entry
Database: PDB / ID: 5drx
TitleCrystal structure of the BCR Fab fragment from subset #4 case CLL240
Components
  • CLL240 BCR light chain
  • CLL240 heavy chain (VH and CH1 domains)
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: 2.104 Å
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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CLL240 heavy chain (VH and CH1 domains)
L: CLL240 BCR light chain
A: CLL240 heavy chain (VH and CH1 domains)
B: CLL240 BCR light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,37210
Polymers97,8194
Non-polymers5536
Water11,656647
1
H: CLL240 heavy chain (VH and CH1 domains)
L: CLL240 BCR light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1865
Polymers48,9102
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-18 kcal/mol
Surface area20300 Å2
MethodPISA
2
A: CLL240 heavy chain (VH and CH1 domains)
B: CLL240 BCR light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1865
Polymers48,9102
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-20 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.187, 92.327, 135.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody CLL240 heavy chain (VH and CH1 domains)


Mass: 24563.494 Da / Num. of mol.: 2
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 CLL240 BCR light chain


Mass: 24346.057 Da / Num. of mol.: 2
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 0.2 M BisTris, 8% (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9726 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 63033 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.28 % / Biso Wilson estimate: 44.67 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.144 / Χ2: 1.088 / Net I/σ(I): 12.34 / Num. measured all: 837112
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.2312.320.6681.231.261212581002998381.28398.1
2.23-2.380.8350.8642.34131207952595220.898100
2.38-2.580.9230.5513.78116670886388590.573100
2.58-2.820.970.3526.59113326815681540.365100
2.82-3.150.9890.20511.5997434743774350.213100
3.15-3.640.9960.12120.2591398659865980.126100
3.64-4.450.9980.08129.6774423560756070.084100
4.45-6.260.9990.06635.858112442144200.068100
6.260.9990.05142.933284260726000.05399.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CLL183 Fab fragment

Resolution: 2.104→46.163 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 3194 5.07 %Random selection
Rwork0.1938 59826 --
obs0.1953 63020 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.65 Å2 / Biso mean: 47.3515 Å2 / Biso min: 17.85 Å2
Refinement stepCycle: final / Resolution: 2.104→46.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6752 0 36 647 7435
Biso mean--57.36 42.54 -
Num. residues----877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097039
X-RAY DIFFRACTIONf_angle_d1.069583
X-RAY DIFFRACTIONf_chiral_restr0.0411061
X-RAY DIFFRACTIONf_plane_restr0.0051225
X-RAY DIFFRACTIONf_dihedral_angle_d13.0772551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1037-2.13510.30121160.29962348246493
2.1351-2.16850.37291390.285425812720100
2.1685-2.2040.33811470.274325792726100
2.204-2.2420.32741150.253525792694100
2.242-2.28280.28291470.249125892736100
2.2828-2.32670.30171250.250425902715100
2.3267-2.37420.29221380.2425832721100
2.3742-2.42580.26331540.244225792733100
2.4258-2.48230.27481340.239725542688100
2.4823-2.54430.30631520.236225962748100
2.5443-2.61310.26971400.24625862726100
2.6131-2.690.2791260.237926012727100
2.69-2.77680.32091620.230525752737100
2.7768-2.8760.26141250.219426342759100
2.876-2.99120.22581400.20925792719100
2.9912-3.12730.22731470.201125922739100
3.1273-3.29210.27821330.199626272760100
3.2921-3.49830.20941340.192326222756100
3.4983-3.76830.18991510.176226252776100
3.7683-4.14730.17981350.159326362771100
4.1473-4.74690.19331560.141326522808100
4.7469-5.97860.15321590.150626692828100
5.9786-46.17460.18171190.192128502969100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.06152.50531.69383.71242.70293.5587-0.020.2062-0.28140.18430.2624-0.55550.23140.5886-0.24720.39080.1076-0.05150.5545-0.07040.491895.379856.70161.3617
24.48220.21-1.0390.9786-0.08111.78730.0609-0.48710.12470.2402-0.02740.0215-0.1181-0.0559-0.01210.45920.028-0.0660.4774-0.0190.443584.626673.999132.4067
34.6231.303-5.48872.6193-2.16018.26540.18780.14150.08770.0265-0.04260.1218-0.2997-0.15930.01670.35910.0024-0.04770.356-0.0170.322869.507661.38221.6988
42.7697-0.1931-0.63572.76140.25322.0619-0.0415-0.1285-0.13630.15180.00120.00670.2437-0.0454-0.00860.34730.0006-0.02460.3862-0.03670.293775.690251.8186-1.0658
52.960.7483-3.76781.1474-0.04545.680.0424-0.314-0.0380.1315-0.0462-0.06790.10410.4769-0.04520.37450.0274-0.03240.4267-0.00530.32977.837657.35461.4228
62.6253-1.8154-1.53724.7865.75837.16970.0183-0.39760.5523-0.0329-0.10640.1543-0.2086-0.10480.0560.4082-0.01810.01890.4509-0.07010.440264.239365.708917.207
73.13365.16460.18189.63681.85664.3126-0.0533-1.41540.2170.5644-0.2578-0.7345-0.37590.1320.26280.55110.0747-0.11450.5514-0.10430.683679.687386.053133.8682
82.91553.56120.64688.03062.80932.819-0.04140.12720.1043-0.3742-0.0998-0.1654-0.2378-0.16560.15610.44650.0768-0.01840.4558-0.03450.482970.789580.402222.6961
91.57060.8038-0.61015.03181.21811.8539-0.04550.1038-0.0326-0.1423-0.152-0.3581-0.0678-0.13030.14980.35520.0073-0.04570.48730.00570.387272.603176.839321.2812
103.55460.62440.56976.11151.00192.66780.0022-0.05770.5657-0.1084-0.18920.0083-0.3355-0.10770.2280.55270.0843-0.0750.4513-0.01930.579471.876989.487227.1736
119.0926-0.1924.15233-0.67014.33950.4832-0.8779-0.611-0.1816-0.02920.38170.4343-0.1363-0.41090.5402-0.008-0.11680.42530.06780.5392121.622355.123443.4377
124.1043-0.10731.63481.8249-1.30073.74910.115-0.0182-0.9701-0.18140.2260.44380.5006-0.4013-0.3880.5332-0.0384-0.12770.43690.02450.6251111.665255.712534.9337
136.764-0.52183.26816.36830.61522.4644-0.0720.1980.20430.31240.3513-0.3949-0.16470.374-0.33480.4391-0.0389-0.04490.48740.00020.4529123.141965.890638.1659
145.56170.59840.23416.4025-0.90755.67440.05460.7728-0.2807-0.59080.1905-0.11160.470.1217-0.28480.48030.0689-0.11480.3919-0.06870.5051119.231258.933427.4116
156.08052.2490.66323.6584-0.17743.58120.07660.4608-0.8761-0.4220.1047-0.38430.55640.4094-0.2150.57220.1396-0.07110.5476-0.10130.5352123.419754.961530.6227
163.8465-0.7073.16391.4208-1.0833.71890.19570.2392-0.459-0.0989-0.07220.06690.31960.2268-0.15380.44930.0492-0.04980.3893-0.03980.4542117.876161.41932.6108
178.7039-3.87335.87885.8201-3.71824.2645-0.0615-0.6273-0.3786-0.02510.25160.2025-0.0917-0.9713-0.28360.3981-0.0197-0.05090.3894-0.0030.4551109.683266.143535.3636
182.4214-0.3815-0.01523.3379-1.10220.9961-0.1655-0.15310.18630.6822-0.0942-0.4162-0.35140.58580.22740.5471-0.0203-0.07080.50560.06960.4268136.237165.240461.9133
191.4654-0.24870.65575.2291-0.3687.2654-0.3787-0.3741-0.051.1642-0.3160.1301-0.3553-0.05770.54270.7254-0.0255-0.07650.547-0.00640.4418130.284772.242866.9321
203.6102-0.87380.52184.38773.20067.1681-0.2514-0.55250.52071.03830.1661-0.6069-0.65350.710.12031.0124-0.0891-0.14050.5650.04570.5567135.60773.827968.8657
212.6227-0.519-0.85926.50252.62694.51130.0773-0.26410.23321.9197-0.2057-0.4627-0.64640.33730.25481.0422-0.0376-0.12550.56980.07710.5081134.429463.439272.1705
220.85270.1176-0.35682.40971.91436.01980.0046-0.07780.0391-0.12630.1892-0.0732-0.21260.4858-0.18480.329-0.0145-0.00590.36350.00670.3298118.604882.578332.3638
234.5742-1.03723.71116.7125-2.09784.8780.0884-0.5615-0.08210.61590.18960.00590.0509-0.505-0.25240.41010.0249-0.02170.3822-0.00360.3451113.40474.443841.2287
241.96760.7902-0.23522.8658-0.25646.5340.028-0.0140.12410.09820.01740.3369-0.3363-0.286-0.04580.31420.0167-0.0270.348-0.00140.3612108.460282.137935.0264
252.0454-1.3356-0.45094.2613.16295.5504-0.0247-0.0113-0.01650.18930.1911-0.00760.21420.1956-0.10260.3382-0.0299-0.02660.38610.00940.3414117.034976.982737.0334
263.2052-1.59391.74391.3374-1.4222.595-0.0051-0.06730.41140.7591-0.5299-1.2024-0.37040.21490.5120.6973-0.1331-0.30580.5160.06530.8597131.756185.461659.1752
276.3135-3.67332.63275.844-0.72382.0079-0.43970.53530.58611.534-0.4021-1.6083-0.19490.52270.87940.695-0.1116-0.23080.69320.21221.0202141.902476.372663.2208
284.56070.10190.26063.45430.69464.714-0.02110.8487-0.5945-0.32830.0873-1.1124-0.77050.59850.11230.878-0.2573-0.12141.04930.23691.1117145.318781.907452.6711
292.1896-2.51810.38286.3027-0.73784.4752-0.1691-0.0598-0.16710.3153-0.0856-0.3364-0.4790.19030.14320.5458-0.0318-0.07970.4984-0.00990.4699131.04379.848158.6089
300.5433-1.01620.12972.02250.52731.4763-0.25690.71850.87050.5106-0.1995-1.63410.06970.81890.36390.7705-0.1682-0.270.99970.39181.555149.943281.249658.5116
311.2783-1.65470.80453.99410.56275.48160.29770.17790.54130.54240.2364-0.56270.29570.8776-0.50110.8062-0.2549-0.47730.86760.17991.6244149.628986.469363.6314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 208 through 219 )H1 - 119
2X-RAY DIFFRACTION2chain 'H' and (resid 120 through 228 )H120 - 228
3X-RAY DIFFRACTION3chain 'L' and (resid 0 through 25 )L0 - 25
4X-RAY DIFFRACTION4chain 'L' and (resid 26 through 80 )L26 - 80
5X-RAY DIFFRACTION5chain 'L' and (resid 81 through 107 )L81 - 107
6X-RAY DIFFRACTION6chain 'L' and (resid 108 through 119 )L108 - 119
7X-RAY DIFFRACTION7chain 'L' and (resid 120 through 134 )L120 - 134
8X-RAY DIFFRACTION8chain 'L' and (resid 135 through 156 )L135 - 156
9X-RAY DIFFRACTION9chain 'L' and (resid 157 through 180 )L157 - 180
10X-RAY DIFFRACTION10chain 'L' and (resid 181 through 220 )L181 - 220
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 17 )A1 - 17
12X-RAY DIFFRACTION12chain 'A' and (resid 18 through 33 )A18 - 33
13X-RAY DIFFRACTION13chain 'A' and (resid 34 through 45 )A34 - 45
14X-RAY DIFFRACTION14chain 'A' and (resid 46 through 59 )A46 - 59
15X-RAY DIFFRACTION15chain 'A' and (resid 60 through 75 )A0
16X-RAY DIFFRACTION16chain 'A' and (resid 76 through 108 )A76 - 108
17X-RAY DIFFRACTION17chain 'A' and (resid 109 through 119 )A109 - 119
18X-RAY DIFFRACTION18chain 'A' and (resid 120 through 164 )A120 - 164
19X-RAY DIFFRACTION19chain 'A' and (resid 165 through 184 )A165 - 184
20X-RAY DIFFRACTION20chain 'A' and (resid 185 through 207 )A185 - 207
21X-RAY DIFFRACTION21chain 'A' and (resid 208 through 226 )A208 - 226
22X-RAY DIFFRACTION22chain 'B' and (resid 0 through 37 )B0 - 37
23X-RAY DIFFRACTION23chain 'B' and (resid 38 through 53 )B38 - 53
24X-RAY DIFFRACTION24chain 'B' and (resid 54 through 80 )B54 - 80
25X-RAY DIFFRACTION25chain 'B' and (resid 81 through 107 )B81 - 107
26X-RAY DIFFRACTION26chain 'B' and (resid 108 through 127 )B108 - 127
27X-RAY DIFFRACTION27chain 'B' and (resid 128 through 147 )B128 - 147
28X-RAY DIFFRACTION28chain 'B' and (resid 148 through 167 )B148 - 167
29X-RAY DIFFRACTION29chain 'B' and (resid 168 through 187 )B168 - 187
30X-RAY DIFFRACTION30chain 'B' and (resid 188 through 207 )B188 - 207
31X-RAY DIFFRACTION31chain 'B' and (resid 208 through 219 )B208 - 219

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