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- PDB-7x0g: Crystal structure of sugar binding protein CbpA from Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 7x0g
TitleCrystal structure of sugar binding protein CbpA from Clostridium thermocellum
ComponentsCbpA
KeywordsSUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / glucose / cellodextrin
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Nov 29, 2023Group: 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
A: CbpA
B: CbpA


Theoretical massNumber of molelcules
Total (without water)61,7552
Polymers61,7552
Non-polymers00
Water5,368298
1
A: CbpA


Theoretical massNumber of molelcules
Total (without water)30,8771
Polymers30,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CbpA


Theoretical massNumber of molelcules
Total (without water)30,8771
Polymers30,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.070, 94.460, 58.500
Angle α, β, γ (deg.)90.000, 114.940, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 32 and (name N or name...
21(chain B and (resid 32 through 34 or (resid 35...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 32 and (name N or name...A32
121(chain A and ((resid 32 and (name N or name...A32 - 319
131(chain A and ((resid 32 and (name N or name...A32 - 319
141(chain A and ((resid 32 and (name N or name...A32 - 319
151(chain A and ((resid 32 and (name N or name...A32 - 319
211(chain B and (resid 32 through 34 or (resid 35...B32 - 34
221(chain B and (resid 32 through 34 or (resid 35...B35
231(chain B and (resid 32 through 34 or (resid 35...B33 - 319
241(chain B and (resid 32 through 34 or (resid 35...B33 - 319
251(chain B and (resid 32 through 34 or (resid 35...B33 - 319
261(chain B and (resid 32 through 34 or (resid 35...B33 - 319

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Components

#1: Protein CbpA


Mass: 30877.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GB CP002416.1 / 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.: 298 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris, pH 8.5, 23% 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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.23 Å / Num. obs: 68775 / % possible obs: 97.5 % / Redundancy: 1.903 % / Biso Wilson estimate: 31.97 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.118 / Χ2: 0.774 / Net I/σ(I): 6.08 / Num. measured all: 130875 / Scaling rejects: 3
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
2.1-2.151.90.2152.989834522751750.8910.2999
2.15-2.211.9010.1973.49546506350220.8990.26799.2
2.21-2.281.9110.1743.989269491148510.9140.23598.8
2.28-2.351.910.1644.079114483147710.9230.22298.8
2.35-2.421.9090.1544.488846469546330.9240.20998.7
2.42-2.511.9060.13858376446743950.9430.18798.4
2.51-2.61.9080.1325.618107436242500.9410.17997.4
2.6-2.711.9040.1186.117694413440400.9490.16197.7
2.71-2.831.9030.1136.67390398038830.9490.15497.6
2.83-2.971.9020.1017.247158386737630.9580.13797.3
2.97-3.131.9020.0977.566669364635070.9580.13396.2
3.13-3.321.9030.0928.116353343033390.960.12697.3
3.32-3.551.8990.0848.45916325131160.9620.11695.8
3.55-3.831.8970.0848.595522302129110.9570.11596.4
3.83-4.21.880.0828.715054278826890.9610.11396.4
4.2-4.71.8460.0728.684468249524210.9730.09997
4.7-5.421.9220.0668.94162220221650.9750.09198.3
5.42-6.641.9510.078.913619188618550.970.09698.4
6.64-9.391.9420.0559.022736144514090.9840.07697.5
9.39-47.231.7970.0578.6510428065800.9790.0872

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H3H

2h3h


Resolution: 2.1→47.23 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 3868 5.62 %
Rwork0.2614 64903 -
obs0.2628 68771 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.68 Å2 / Biso mean: 56.1017 Å2 / Biso min: 17.66 Å2
Refinement stepCycle: final / Resolution: 2.1→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 0 298 4532
Biso mean---44.88 -
Num. residues----575
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1728X-RAY DIFFRACTION4.518TORSIONAL
12B1728X-RAY DIFFRACTION4.518TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12560.38541380.3338232099
2.1256-2.15250.37411500.3252238499
2.1525-2.18090.36941470.3362358100
2.1809-2.21070.3571250.34082333100
2.2107-2.24230.31781460.318236599
2.2423-2.27580.3621150.3093234199
2.2758-2.31140.38121550.328233799
2.3114-2.34920.33461600.3121233599
2.3492-2.38980.37551110.3211236699
2.3898-2.43320.32751620.3212237399
2.4332-2.480.33851270.3114227899
2.48-2.53060.34991360.2874234298
2.5306-2.58560.33391320.3052234998
2.5856-2.64580.30361410.3001229598
2.6458-2.71190.36031490.2831229797
2.7119-2.78530.31481320.2984238698
2.7853-2.86720.29251400.2747229298
2.8672-2.95970.30861220.2855228097
2.9597-3.06550.34721380.2927231797
3.0655-3.18820.32791340.2761226597
3.1882-3.33330.32911390.2722232797
3.3333-3.5090.27591400.2524229397
3.509-3.72870.28521410.2389224996
3.7287-4.01650.23121330.2338231797
4.0165-4.42040.22831330.2216229397
4.4204-5.05940.20891480.1941232298
5.0594-6.37190.23551380.2415233699
6.3719-47.20.2241360.1974215390
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)
12.7881-0.0573-1.06060.8181.15632.06830.0902-1.58821.55290.16060.0335-0.1026-0.21160.4319-0.18480.3169-0.02660.03950.8314-0.40360.703313.662-25.6379.57
22.6696-1.22640.67375.57670.66537.3145-0.1485-0.1126-0.11960.14940.0597-0.30840.6190.46680.06990.3591-0.01290.08950.23040.04090.230914.901-51.392-10.531
34.0532-0.4183-0.89183.26151.39553.84690.0336-0.13360.8473-0.20110.2265-0.3588-0.10890.2092-0.29320.2725-0.03650.02520.1966-0.00970.361612.731-32.347-7.686
40.2251-0.19750.15680.3105-0.38520.54890.7793-0.1326-0.6230.32830.48380.61091.0013-0.7627-0.82331.281-0.5675-0.52080.70320.3981.121435.598-57.11221.638
51.22581.70250.88173.2805-0.34453.62270.5687-0.8506-0.5773-0.08010.210.44011.1093-1.8345-0.6080.7077-0.3778-0.21910.89710.31730.653933.036-48.88722.866
63.6716-0.9024-0.67554.69590.48892.4696-0.11840.11410.0356-0.34170.05720.14120.1862-0.13510.05580.4116-0.08870.07830.2583-0.02490.22848.085-27.2456.365
70.1492-0.28130.60871.0663-0.10084.15470.8045-0.2618-0.933-0.25020.5181-0.07740.9171-1.1468-0.39670.9349-0.3199-0.41030.51010.29590.848744.562-53.13227.719
81.8864-0.13150.20071.2903-1.47766.06850.07930.3054-0.4059-0.14060.0494-0.22511.0962-0.0599-0.07960.4362-0.04910.03740.2209-0.03880.469550.097-44.2078.243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 32:143 )A32 - 143
2X-RAY DIFFRACTION2( CHAIN A AND RESID 144:243 )A144 - 243
3X-RAY DIFFRACTION3( CHAIN A AND RESID 244:319 )A244 - 319
4X-RAY DIFFRACTION4( CHAIN B AND RESID 33:51 )B33 - 51
5X-RAY DIFFRACTION5( CHAIN B AND RESID 52:143 )B52 - 143
6X-RAY DIFFRACTION6( CHAIN B AND RESID 144:274 )B144 - 274
7X-RAY DIFFRACTION7( CHAIN B AND RESID 275:300 )B275 - 300
8X-RAY DIFFRACTION8( CHAIN B AND RESID 301:319 )B301 - 319

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