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- PDB-7x0k: Crystal structure of sugar binding protein CbpB complexed wtih ce... -

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Basic information

Entry
Database: PDB / ID: 7x0k
TitleCrystal structure of sugar binding protein CbpB complexed wtih cellotriose from Clostridium thermocellum
ComponentsCpbB
KeywordsSUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / cellodextrin
Function / homologybeta-cellotriose
Function and homology information
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDong, S. / Yao, X. / Feng, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070125 China
National Natural Science Foundation of China (NSFC)32170051 China
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: Mbio / Year: 2022
Title: Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum.
Authors: Yan, F. / Dong, S. / Liu, Y.J. / Yao, X. / Chen, C. / Xiao, Y. / Bayer, E.A. / Shoham, Y. / You, C. / Cui, Q. / Feng, Y.
History
DepositionFeb 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CpbB
B: CpbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7204
Polymers91,7112
Non-polymers1,0092
Water16,988943
1
A: CpbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3602
Polymers45,8551
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CpbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3602
Polymers45,8551
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.440, 44.150, 113.060
Angle α, β, γ (deg.)90.000, 103.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CpbB


Mass: 45855.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 943 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium phosphate monobasic, pH 4.6, 22% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→40.958 Å / Num. obs: 136991 / % possible obs: 95.6 % / Redundancy: 3.485 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.133 / Χ2: 1.099 / Net I/σ(I): 6.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.743.4970.8091.543529110539100920.6030.9595.8
1.74-1.793.3680.6761.79333661038899060.6750.79895.4
1.79-1.843.2750.5442.17313071007595600.7340.64894.9
1.84-1.93.5530.442.8933232971693540.8260.51696.3
1.9-1.963.590.3523.5932783948991320.8930.41196.2
1.96-2.033.5020.284.3130824913288030.9240.32996.4
2.03-2.113.4450.2245.2229439892185460.9450.26395.8
2.11-2.193.2580.1885.8525553842678430.9590.22393.1
2.19-2.293.5380.1666.928032819179240.9670.19596.7
2.29-2.43.5660.1527.4526732776674970.9740.17896.5
2.4-2.533.5450.1288.5125259738371250.9790.1596.5
2.53-2.693.5190.1159.2823666703267250.9820.13695.6
2.69-2.873.3510.09710.2320549660961320.9840.11692.8
2.87-3.13.6220.08811.9321561611859530.9880.10397.3
3.1-3.43.5560.07813.3419449566354700.990.09196.6
3.4-3.83.5430.07314.517034507448080.9890.08594.8
3.8-4.393.4220.06714.9714269451241700.990.07892.4
4.39-5.383.6810.06715.9713565379036850.9910.07897.2
5.38-7.63.6350.07215.8910014294027550.9890.08493.7
7.6-40.9583.6170.07316.965451159715070.9890.08694.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→40.958 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 3852 2.81 %
Rwork0.1796 133139 -
obs0.1806 136991 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.61 Å2 / Biso mean: 21.8061 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 1.7→40.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 132 943 7368
Biso mean--18.98 29.32 -
Num. residues----813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72070.29181340.2685466696
1.7207-1.74250.31561280.2601479696
1.7425-1.76550.32841570.2637477296
1.7655-1.78960.30851260.2507472695
1.7896-1.81520.26841500.2434463394
1.8152-1.84230.28111310.2354488596
1.8423-1.87110.25561410.2163473296
1.8711-1.90180.2241540.2088474496
1.9018-1.93460.23941310.2029486196
1.9346-1.96970.25381340.1986468796
1.9697-2.00760.25861350.2018488397
2.0076-2.04860.2271240.1862478897
2.0486-2.09310.23261590.1828477996
2.0931-2.14180.24241310.1806467495
2.1418-2.19540.23441270.1853458892
2.1954-2.25470.21161350.1716480197
2.2547-2.32110.21951380.1722490097
2.3211-2.3960.19131390.1713474996
2.396-2.48160.22561320.1682480696
2.4816-2.5810.22151470.1689483897
2.581-2.69840.20991490.1728465995
2.6984-2.84060.24361290.1781460592
2.8406-3.01860.20531470.182483197
3.0186-3.25150.21691220.1687483897
3.2515-3.57860.18011490.1583479696
3.5786-4.0960.15331290.1482460292
4.096-5.15890.1951400.1477477997
5.1589-40.90.19451340.1882472194
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)
12.47670.1252-1.90751.31460.76752.6334-0.2680.2107-0.25960.0392-0.2002-0.05070.46020.03360.4290.16530.01350.01740.10640.00320.1958-15.09346.424837.4875
21.11210.38060.29081.63791.15861.97130.03820.1899-0.1552-0.20560.0605-0.02590.01530.027-0.11410.2101-0.00230.00520.1891-0.01630.171120.223428.1119.0598
31.90140.4009-0.00232.7166-0.09642.4258-0.03890.19530.1031-0.17820.09440.1988-0.2417-0.1766-0.04420.14050.0133-0.00070.16310.01640.14345.89632.077712.9894
40.44150.22190.13661.4075-0.88642.04080.04950.11610.0002-0.135-0.03030.10650.11640.0762-0.05050.0856-00.00980.1145-0.03590.14079.731919.377524.3632
50.8960.19320.03451.9101-0.33041.5815-0.0431-0.0697-0.16980.1058-0.0043-0.37250.17510.23010.05410.12180.032-0.00050.1649-0.00390.18617.006311.972741.8983
61.2055-0.1087-0.41770.90540.18060.78490.02780.0172-0.0241-0.0468-0.0414-0.09240.07650.08270.00560.09840.00210.00520.11580.0040.120313.809519.405335.1972
71.39560.13490.08852.7255-0.91692.13620.01780.17890.0785-0.34260.08270.0781-0.05530.0391-0.08390.1512-0.01640.00670.1105-0.00390.09511.748225.35136.7747
80.4383-0.1289-0.07150.0390.05631.004-0.01570.0124-0.0339-0.01760.0453-0.03610.02220.0791-0.02920.12040.00480.00960.13760.0040.17058.97720.72925.997
92.5389-1.68520.50082.0567-1.40791.82170.1336-0.01540.2347-0.1783-0.0208-0.14870.05820.0944-0.05490.2071-0.04060.00860.1956-0.06110.20810.143935.991245.1815
101.7997-0.10010.12211.2342-0.13521.32390.06250.20610.0613-0.1732-0.04730.03920.07840.0106-0.01550.14970.0048-0.00030.138-0.00470.0866-28.216225.97913.5872
110.40180.09840.17320.56850.42981.94980.02210.08980.0304-0.1150.01490.0128-0.00580.0731-0.06370.07890.00470.00540.07060.02030.1413-21.162830.719129.8298
122.04870.53790.22051.08520.62481.75710.05620.04960.03410.0384-0.00340.0408-0.0157-0.1031-0.05930.08680.01470.00820.07260.02420.1048-24.74931.037850.2289
131.0903-0.6749-0.0740.84740.13620.33830.04640.03040.0297-0.0343-0.04040.0451-0.0528-0.0244-0.00580.1248-0.0042-0.00130.0951-0.00090.1276-23.333125.979339.8703
140.9866-0.0509-0.00151.88661.11421.79660.02740.22140.0527-0.3257-0.05390.0077-0.166-0.01530.02870.14050.0142-0.02440.13570.01470.0845-26.362731.718211.4496
150.1398-0.12480.2130.2409-0.51990.9031-0.01880.0250.02820.00410.03770.0376-0.0064-0.0725-0.01950.1482-0.00390.00210.1165-0.00050.1601-21.2926.432232.9207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 436 through 455 )B436 - 455
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 103 )A49 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 147 )A104 - 147
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 177 )A148 - 177
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 219 )A178 - 219
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 332 )A220 - 332
7X-RAY DIFFRACTION7chain 'A' and (resid 333 through 369 )A333 - 369
8X-RAY DIFFRACTION8chain 'A' and (resid 370 through 427 )A370 - 427
9X-RAY DIFFRACTION9chain 'A' and (resid 428 through 454 )A428 - 454
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 147 )B49 - 147
11X-RAY DIFFRACTION11chain 'B' and (resid 148 through 177 )B148 - 177
12X-RAY DIFFRACTION12chain 'B' and (resid 178 through 218 )B178 - 218
13X-RAY DIFFRACTION13chain 'B' and (resid 219 through 332 )B219 - 332
14X-RAY DIFFRACTION14chain 'B' and (resid 333 through 369 )B333 - 369
15X-RAY DIFFRACTION15chain 'B' and (resid 370 through 435 )B370 - 435

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