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- PDB-7x0l: Crystal structure of sugar binding protein CbpB complexed wtih ce... -

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Basic information

Entry
Database: PDB / ID: 7x0l
TitleCrystal structure of sugar binding protein CbpB complexed wtih cellotetraose from Clostridium thermocellum
ComponentsCbpB
KeywordsSUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / cellodextrin
Function / homologybeta-cellotetraose
Function and homology information
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: CbpB
B: CbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8254
Polymers90,4922
Non-polymers1,3332
Water10,431579
1
A: CbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9122
Polymers45,2461
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9122
Polymers45,2461
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.070, 46.560, 119.100
Angle α, β, γ (deg.)90.000, 107.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CbpB


Mass: 45245.770 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-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris, pH5.5, 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: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→38.555 Å / Num. obs: 112089 / % possible obs: 96.4 % / Redundancy: 3.086 % / Biso Wilson estimate: 17 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.179 / Χ2: 0.954 / Net I/σ(I): 8.15 / Num. measured all: 345880 / Scaling rejects: 1211
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
1.9-1.952.8740.9842.4521898866076190.5741.21688
1.95-22.9210.8293.0922513829777070.6621.01992.9
2-2.062.9230.4934.2222839820178130.7970.60695.3
2.06-2.122.860.4234.9121713800175910.8120.5294.9
2.12-2.193.0190.3515.8422236760273650.8680.42796.9
2.19-2.273.2130.3426.4623411738272860.8930.41198.7
2.27-2.363.2340.2887.0222856717670680.9180.34598.5
2.36-2.453.2110.2387.5322050692868670.9420.28599.1
2.45-2.563.1770.2068.0620650660164990.9490.24898.5
2.56-2.693.170.1738.6819598626461830.9610.20898.7
2.69-2.833.130.1469.4418525601159180.9640.17798.5
2.83-32.9910.1269.9716503568155170.9690.15397.1
3-3.213.0130.111.0615364534851000.9810.12295.4
3.21-3.473.3340.08512.8816362493949080.9860.10199.4
3.47-3.83.2840.07813.8714985461545630.9870.09298.9
3.8-4.253.2560.07314.5913393416541130.9880.08798.8
4.25-4.913.1270.06814.7811065358935390.9880.08298.6
4.91-6.012.9660.06614.418435308228440.9880.0892.3
6.01-8.53.2730.06615.627676237823450.990.07898.6
8.5-38.5553.0610.07815.883808131212440.9820.09394.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.555 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 3816 3.41 %
Rwork0.1744 108228 -
obs0.1755 112044 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.01 Å2 / Biso mean: 26.5204 Å2 / Biso min: 4.22 Å2
Refinement stepCycle: final / Resolution: 1.9→38.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6334 0 90 579 7003
Biso mean--24.53 31.4 -
Num. residues----818
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.9240.46181310.4662361687
1.924-1.94940.6571340.5555371688
1.9494-1.97610.34581300.3677371691
1.9761-2.00430.36061420.2983396195
2.0043-2.03420.23761480.2355394695
2.0342-2.0660.25041330.2234398096
2.066-2.09990.26141440.2084400196
2.0999-2.13610.25661340.192385593
2.1361-2.17490.19871430.1909399397
2.1749-2.21670.23311500.1897414899
2.2167-2.2620.21351370.191409599
2.262-2.31110.23141460.1809406898
2.3111-2.36490.1961410.1612411299
2.3649-2.4240.19541440.1592410399
2.424-2.48960.19161400.1539412699
2.4896-2.56280.18411500.1493413698
2.5628-2.64550.19571270.1453405898
2.6455-2.740.19121480.1502414999
2.74-2.84970.20561330.1573406999
2.8497-2.97940.20561500.1587405898
2.9794-3.13640.21161340.1566390594
3.1364-3.33280.20441480.1491412299
3.3328-3.58990.17441470.1414413799
3.5899-3.95090.16141440.1269408799
3.9509-4.52180.15431500.129410999
4.5218-5.69410.16141430.1367401297
5.6941-38.50.1611450.1796395095
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)
11.1140.3726-0.42542.6809-0.771.50320.0551-0.134-0.02580.145-0.03940.0621-0.0084-0.0443-0.02910.0887-0.0142-0.00080.138-0.02590.1353-9.01237.701144.2027
20.65740.15780.57820.89230.91323.5772-0.03870.0526-0.0227-0.0869-0.00410.02570.07440.07580.01280.08520.00960.00180.0677-0.0120.1607-3.70063.421221.7462
33.14120.03690.38733.73351.44424.3732-0.0260.24290.2043-0.2089-0.04780.3431-0.0378-0.4191-0.0150.12080.0046-0.04020.10740.00820.1693-11.41088.91536.7695
41.18920.5834-0.12461.03360.29690.5706-0.02410.0313-0.0125-0.0146-0.03360.14080.0202-0.08810.04510.09970.0252-0.00780.096-0.01020.1643-6.902710.649517.5907
50.97190.31320.06453.92561.90364.79480.0328-0.1863-0.07620.2474-0.21630.03510.2505-0.08170.14350.0145-0.01890.00710.12410.02540.1487-7.29731.738645.4462
60.5320.1625-0.15021.173-0.36540.26630.00260.02420.0486-0.05350.01370.14730.0102-0.0215-0.01320.13340.0084-0.00560.1107-0.01330.1726-2.261214.511123.9553
70.98520.06950.51511.50840.46412.89030.0746-0.0116-0.12970.0554-0.0350.00320.1690.184-0.05540.12140.03930.00740.13670.04410.1603-40.46122.18841.8661
80.6750.3918-0.5761.6113-1.37052.3434-0.0256-0.00730.0466-0.0464-0.0183-0.1675-0.06570.15090.00270.09260.00350.00770.1052-0.01980.1621-38.782624.826117.6313
91.62140.4490.16191.37790.10670.5288-0.0215-0.0457-0.0802-0.00530.0019-0.18960.00660.07240.01650.09960.02650.0010.1052-0.00230.1161-41.209616.130919.3308
100.32470.17050.02010.1388-0.1882.5127-0.0135-0.0284-0.0585-0.02220.0004-0.01320.0690.07930.01510.09530.0440.00280.12210.00920.1395-44.32928.4529.1897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 147 )A49 - 147
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 187 )A148 - 187
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 218 )A188 - 218
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 332 )A219 - 332
5X-RAY DIFFRACTION5chain 'A' and (resid 333 through 369 )A333 - 369
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 457 )A370 - 457
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 157 )B49 - 157
8X-RAY DIFFRACTION8chain 'B' and (resid 158 through 218 )B158 - 218
9X-RAY DIFFRACTION9chain 'B' and (resid 219 through 332 )B219 - 332
10X-RAY DIFFRACTION10chain 'B' and (resid 333 through 457 )B333 - 457

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