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- PDB-7x0o: Crystal structure of sugar binding protein CbpC from Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 7x0o
TitleCrystal structure of sugar binding protein CbpC from Clostridium thermocellum
ComponentsCbpC
KeywordsSUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / cellodextrin
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CbpC
B: CbpC


Theoretical massNumber of molelcules
Total (without water)99,5542
Polymers99,5542
Non-polymers00
Water7,152397
1
A: CbpC


Theoretical massNumber of molelcules
Total (without water)49,7771
Polymers49,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CbpC


Theoretical massNumber of molelcules
Total (without water)49,7771
Polymers49,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.810, 80.060, 170.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 7 and (name N or name...
21(chain B and (resid 7 through 168 or (resid 169...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 7 and (name N or name...A7
121(chain A and ((resid 7 and (name N or name...A33 - 460
131(chain A and ((resid 7 and (name N or name...A33 - 460
141(chain A and ((resid 7 and (name N or name...A33 - 460
151(chain A and ((resid 7 and (name N or name...A33 - 460
211(chain B and (resid 7 through 168 or (resid 169...B7 - 168
221(chain B and (resid 7 through 168 or (resid 169...B169
231(chain B and (resid 7 through 168 or (resid 169...B33 - 460
241(chain B and (resid 7 through 168 or (resid 169...B33 - 460
251(chain B and (resid 7 through 168 or (resid 169...B33 - 460
261(chain B and (resid 7 through 168 or (resid 169...B33 - 460

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Components

#1: Protein CbpC


Mass: 49776.898 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M BIS-TRIS pH 5.5, 25% 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: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→42.587 Å / Num. obs: 103492 / % possible obs: 85.6 % / Redundancy: 3.527 % / Biso Wilson estimate: 32.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.102 / Χ2: 1.116 / Net I/σ(I): 9.5 / Num. measured all: 365052 / Scaling rejects: 19
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
2-2.052.4820.6881.4713914894056060.4410.84562.7
2.05-2.113.1440.5262.5212650872540240.7080.62346.1
2.11-2.173.3870.453.2628318844983600.8020.5398.9
2.17-2.243.310.6082.5218771825156710.8490.71668.7
2.24-2.313.2650.4832.999129794727960.8710.56835.2
2.31-2.393.5320.2615.3127284777077240.9360.30799.4
2.39-2.483.5790.2186.0726538745974150.9450.25599.4
2.48-2.583.6370.1787.3726003718471490.9610.20999.5
2.58-2.73.6190.1618.4924784690068480.960.18999.2
2.7-2.833.7230.1269.9524431658465630.9750.14899.7
2.83-2.983.7450.10611.3723265623262130.9850.12499.7
2.98-3.163.770.08913.5822241590959000.9870.10499.8
3.16-3.383.7450.0815.1820845558355660.9880.09399.7
3.38-3.653.6330.07915.8117215515147380.9870.09392
3.65-43.5790.07316.7713860477838730.9870.08681.1
4-4.473.6770.06618.0515746429642820.9890.07899.7
4.47-5.163.6540.06418.4413776378037700.990.07599.7
5.16-6.323.6960.05918.1711801319631930.9920.06999.9
6.32-8.943.8590.05218.939609249024900.9960.061100
8.94-42.5873.7160.04519.324872134613110.9950.05297.4

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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: 2→42.587 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 3755 3.63 %
Rwork0.2313 99726 -
obs0.2323 103481 85.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.78 Å2 / Biso mean: 41.1217 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 2→42.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6637 0 0 397 7034
Biso mean---40.1 -
Num. residues----840
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2528X-RAY DIFFRACTION1.891TORSIONAL
12B2528X-RAY DIFFRACTION1.891TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0001-2.02540.38441440.3593382690
2.0254-2.05210.3809590.3764157780
2.0521-2.08020.320174
2.0802-2.10990.34581540.3308408194
2.1099-2.14140.39221590.3159423499
2.1414-2.17490.3091640.2982428399
2.1749-2.21050.35191630.3196427299
2.2105-2.24860.4104190.356451465
2.2486-2.28950.345290.353776978
2.2895-2.33360.32711590.2984428999
2.3336-2.38120.33751610.28114281100
2.3812-2.4330.34581630.271429099
2.433-2.48960.30271600.27584282100
2.4896-2.55180.3141640.2556428999
2.5518-2.62080.30061620.2503435099
2.6208-2.69790.29761640.2505429199
2.6979-2.7850.27561640.25134225100
2.785-2.88450.30741610.25144311100
2.8845-2.99990.24181690.24534336100
2.9999-3.13640.29291590.23044286100
3.1364-3.30170.26421590.22864327100
3.3017-3.50850.21731610.2261431699
3.5085-3.77920.24551210.2167310372
3.7792-4.15930.23011590.197426599
4.1593-4.76040.20221570.18334319100
4.7604-5.9950.22221600.19264292100
5.995-42.50.20141610.1953431199
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)
10.35610.15320.00350.87430.82272.1974-0.02030.0437-0.06580.118-0.01270.09010.0222-0.01090.05820.2094-0.0258-0.00350.26350.04190.3822-9.95120.9-34.04
22.34750.40670.45490.90420.41451.8611-0.0412-0.15220.29710.0645-0.06640.0941-0.12720.00140.10960.2415-0.0124-0.01310.25810.05440.2943-13.7831.273-6.164
31.53530.53950.0251.72471.47053.9679-0.0256-0.1559-0.08440.17520.0815-0.1492-0.10290.3408-0.04330.22870.02340.00250.23290.07150.3187-3.21425.068-22.269
42.561-0.3104-0.09191.93210.27331.7993-0.0402-0.0743-0.07580.17650.11530.2359-0.15290.0852-0.03630.2627-0.04740.02380.22360.07710.1816-0.53625.423-18.827
54.112-0.31870.07762.51960.87482.75240.12460.6539-0.2679-0.0433-0.18550.3587-0.0561-0.2864-0.01420.1655-0.00020.00060.4195-0.02580.335-22.91560.98-44.817
61.46310.1679-1.11511.8295-0.99174.63250.0441-0.3298-0.14080.58420.13850.098-0.02010.0476-0.25230.3659-0.01440.00620.3054-0.00250.3372-25.15770.369-22.779
73.25140.134-0.78110.5754-0.26471.547-0.02040.09260.12020.33440.13240.11440.0521-0.1825-0.11430.4895-0.0626-0.01130.22690.07050.2597-17.58559.502-12.676
83.3433-0.2714-0.45022.3761-0.85812.30930.04590.32740.09270.411-0.10530.0262-0.1965-0.13170.14610.256-0.0292-0.02610.19290.04960.3384-31.06760.992-17.475
91.63410.1140.77762.5108-0.79842.5912-0.0273-0.00590.08910.43060.03780.14870.0175-0.1870.00040.3603-0.04620.03050.137-0.03190.2344-31.87265.434-29.272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 33:170 )A33 - 170
2X-RAY DIFFRACTION2( CHAIN A AND RESID 171:272 )A171 - 272
3X-RAY DIFFRACTION3( CHAIN A AND RESID 273:355 )A273 - 355
4X-RAY DIFFRACTION4( CHAIN A AND RESID 356:434 )A356 - 434
5X-RAY DIFFRACTION5( CHAIN B AND RESID 33:111 )B33 - 111
6X-RAY DIFFRACTION6( CHAIN B AND RESID 112:194 )B112 - 194
7X-RAY DIFFRACTION7( CHAIN B AND RESID 195:272 )B195 - 272
8X-RAY DIFFRACTION8( CHAIN B AND RESID 273:327 )B273 - 327
9X-RAY DIFFRACTION9( CHAIN B AND RESID 328:434 )B328 - 434

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