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Basic information

Entry
Database: PDB / ID: 7x0m
TitleCrystal structure of sugar binding protein CbpB complexed wtih cellopentaose from Clostridium thermocellum
ComponentsCbpB
KeywordsSUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / cellodextrin
Function / homologybeta-cellopentaose
Function and homology information
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)92,1494
Polymers90,4922
Non-polymers1,6572
Water10,701594
1
A: CbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0742
Polymers45,2461
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0742
Polymers45,2461
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.320, 46.510, 119.380
Angle α, β, γ (deg.)90.000, 107.610, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 49 through 454)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 49 - 454 / Label seq-ID: 1 - 406

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2(chain B and resid 49 through 454)BB

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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- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][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.: 594 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Sodium acetate, pH 4.5, 20% 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: 2→38.555 Å / Num. obs: 83500 / % possible obs: 83.3 % / Redundancy: 1.906 % / Biso Wilson estimate: 18.53 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.162 / Χ2: 0.915 / Net I/σ(I): 7.12 / Num. measured all: 159133 / Scaling rejects: 6
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
2-2.052.0050.4663.9812996738264810.530.63387.8
2.05-2.112.0040.4274.3112692723763340.5880.57887.5
2.11-2.171.9770.3494.6712181698761610.6640.47688.2
2.17-2.241.9450.3554.868525684743830.720.48164
2.24-2.311.8330.3954.666891662037590.7160.5456.8
2.31-2.391.8080.2245.4310344641457220.8480.30689.2
2.39-2.481.8650.1925.9510377618955650.8790.26389.9
2.48-2.582.0090.1626.810732596153410.9180.22189.6
2.58-2.71.9770.1457.1710123566651210.9340.19990.4
2.7-2.831.970.1257.859580541948620.9440.17189.7
2.83-2.981.9460.1128.398967522446070.9520.15388.2
2.98-3.161.8960.0988.957936487841850.9640.13585.8
3.16-3.381.720.0859.076861461939890.9730.11786.4
3.38-3.651.710.089.486000427435080.970.11182.1
3.65-41.9110.07410.825769395730190.9760.10376.3
4-4.471.9240.06311.655505356128610.980.08780.3
4.47-5.161.8560.06211.544808317425900.9810.08681.6
5.16-6.321.6850.06210.683831263122730.980.08786.4
6.32-8.941.7740.05511.413170204217870.9870.07787.5
8.94-38.5551.9380.05312.67184511299520.9850.07484.3

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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: 2→38.555 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 3491 4.18 %
Rwork0.1782 79996 -
obs0.1795 83487 83.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.71 Å2 / Biso mean: 22.5982 Å2 / Biso min: 5.58 Å2
Refinement stepCycle: final / Resolution: 2→38.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 112 594 7000
Biso mean--33.4 31.01 -
Num. residues----814
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2436X-RAY DIFFRACTION1.076TORSIONAL
12B2436X-RAY DIFFRACTION1.076TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02740.24691350.2125337388
2.0274-2.05640.26231460.218329188
2.0564-2.08710.21611540.219339188
2.0871-2.11970.2171490.2209335787
2.1197-2.15440.22161490.211338289
2.1544-2.19160.25731510.206337687
2.1916-2.23140.2371990.221220279
2.2314-2.27430.262440.2277104481
2.2743-2.32080.24741540.213341587
2.3208-2.37120.19811450.2069338590
2.3712-2.42640.24851570.2093341289
2.4264-2.4870.22851480.2019348190
2.487-2.55430.27911430.1943344591
2.5543-2.62940.24011510.1919343890
2.6294-2.71420.21531520.1727350490
2.7142-2.81120.19531560.1803342490
2.8112-2.92380.21371510.1781342188
2.9238-3.05680.22291450.1834331387
3.0568-3.21780.19531460.1764330086
3.2178-3.41930.20871490.1757333587
3.4193-3.68320.21161350.1849300278
3.6832-4.05340.19911210.1508301479
4.0534-4.63910.17751390.134313381
4.6391-5.84160.15721280.1419321983
5.8416-38.50.15891440.1424333987
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)
11.39660.18960.19542.8232.50872.2364-0.001-0.1895-0.00310.10150.1854-0.3521-0.33560.6409-0.15350.2005-0.0796-0.05010.2780.0010.189616.3669-3.17944.6791
21.51050.25860.60612.25240.35892.3620.0302-0.2838-0.08210.263-0.06970.03190.07890.01320.03510.114-0.02580.01680.1640.04080.09065.1072-12.261544.4251
30.93410.0039-0.25660.8513-0.2513.290.0408-0.04510.00960.0008-0.050.0021-0.24390.0728-0.01570.06840.0041-0.02190.03170.00820.12633.5412-6.362326.7479
43.5417-0.0394-0.73523.069-0.72893.3649-0.01540.32790.1731-0.1713-0.0428-0.1959-0.14540.18640.01280.1108-0.02470.01410.1223-0.02640.10819.1317-8.08836.8359
51.91371.08270.08421.554-0.24421.130.02660.0191-0.0138-0.0149-0.0543-0.1174-0.0380.10190.01140.07380.0270.01020.0721-0.00060.09017.9802-12.797117.928
61.2170.20910.43010.76030.46941.69850.0215-0.11230.11920.0641-0.0107-0.0527-0.10910.09780.01160.0971-0.0175-0.00190.0813-0.0010.1084.2487-1.619936.5452
71.13440.4185-0.08920.52610.15651.3035-0.03990.0259-0.1610.02110.0106-0.09680.10750.08430.0540.09380.0143-0.00040.0912-0.0030.1141.7384-21.249221.6985
81.50420.3138-1.31831.3896-1.01374.02280.0197-0.06860.14850.10460.01460.1037-0.148-0.3801-0.04330.11450.0539-0.01520.2068-0.03720.133234.176-4.073542.0272
92.4162-2.37570.64562.4125-0.72272.84-0.0079-0.17010.29120.0602-0.0649-0.4838-0.10150.19130.06470.1003-0.00630.00130.2421-0.03880.227751.1024-4.696842.6011
101.11120.03070.82290.89681.37212.80160.01410.0002-0.05860.12290.0597-0.10750.12550.0697-0.06220.07090.0350.01310.08310.00940.110643.8637-17.015329.9678
113.73820.3032-0.09334.60150.45452.8439-0.1060.0354-0.2857-0.17550.06320.07090.145-0.19350.02350.12630.0050.01590.11290.02130.05638.6652-27.63312.9763
122.38930.7251-0.33031.522-0.03370.7383-0.038-0.02280.0553-0.0317-0.02440.08060.0227-0.06610.04020.10710.0301-0.00180.08340.00570.084341.155-17.810219.2899
131.60230.41560.23183.85570.63443.44710.0032-0.31410.06310.2364-0.03530.03970.1928-0.0486-0.02460.07930.05190.00980.1721-0.01880.119141.2669-11.199245.6312
140.8165-0.012-0.02640.9410.33271.8689-0.02890.00280.06710.02510.08650.0668-0.1356-0.0919-0.05990.11650.04530.01110.11730.01770.138345.5188-10.356519.1227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 77 )A49 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 147 )A78 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 177 )A148 - 177
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 218 )A178 - 218
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 319 )A219 - 319
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 386 )A320 - 386
7X-RAY DIFFRACTION7chain 'A' and (resid 387 through 454 )A387 - 454
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 121 )B49 - 121
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 147 )B122 - 147
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 177 )B148 - 177
11X-RAY DIFFRACTION11chain 'B' and (resid 178 through 218 )B178 - 218
12X-RAY DIFFRACTION12chain 'B' and (resid 219 through 332 )B219 - 332
13X-RAY DIFFRACTION13chain 'B' and (resid 333 through 380 )B333 - 380
14X-RAY DIFFRACTION14chain 'B' and (resid 381 through 454 )B381 - 454

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