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- PDB-7x0p: Crystal structure of sugar binding protein CbpD from Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 7x0p
TitleCrystal structure of sugar binding protein CbpD from Clostridium thermocellum
ComponentsCbpD
KeywordsSUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / cellodextrin
Function / homology: / Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / outer membrane-bounded periplasmic space / carbohydrate binding / Periplasmic binding protein domain-containing protein
Function and homology information
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Assembly

Deposited unit
A: CbpD


Theoretical massNumber of molelcules
Total (without water)37,5001
Polymers37,5001
Non-polymers00
Water6,539363
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.910, 63.170, 69.700
Angle α, β, γ (deg.)90.000, 106.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

21A-496-

HOH

31A-529-

HOH

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Components

#1: Protein CbpD / Peripla_BP_4 domain-containing protein


Mass: 37500.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_2446 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DI69
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
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: BL17U1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→33.467 Å / Num. obs: 86939 / % possible obs: 94.7 % / Redundancy: 1.925 % / Biso Wilson estimate: 19.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.059 / Χ2: 0.977 / Net I/σ(I): 10.3 / Num. measured all: 167390 / Scaling rejects: 32
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
1.5-1.541.9370.5131.9112483676764430.6850.68595.2
1.54-1.581.9460.4222.2912416669463800.7660.56495.3
1.58-1.631.9460.3522.8111951641161400.8050.47295.8
1.63-1.681.9430.283.4811634624459880.8710.37795.9
1.68-1.731.9440.2324.2511269602957960.9010.31396.1
1.73-1.791.9460.1655.410946585456260.9470.22296.1
1.79-1.861.9430.1356.7310556564554330.960.18296.2
1.86-1.941.9270.1028.69889544751320.9790.13994.2
1.94-2.021.9350.07510.429720523050240.9880.10296.1
2.02-2.121.930.05912.479213498647730.9920.0895.7
2.12-2.241.9250.05214.68725478845320.9910.07194.7
2.24-2.371.920.04716.447922448441260.9920.06492
2.37-2.541.9240.03917.37748419240270.9940.05496.1
2.54-2.741.9080.03618.827184393337650.9950.0595.7
2.74-31.9020.03520.636523361534300.9950.04794.9
3-3.351.8870.03122.285821329330840.9950.04393.7
3.35-3.871.8360.02922.974725284425740.9950.0490.5
3.87-4.741.8780.02623.854225244922500.9950.03691.9
4.74-6.711.8710.02423.523303186017650.9960.03494.9
6.71-33.4671.7470.02323113710396510.9960.03362.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XSS

5xss


Resolution: 1.5→33.467 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 3857 4.44 %
Rwork0.1698 83062 -
obs0.1711 86919 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.52 Å2 / Biso mean: 36.4131 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 1.5→33.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 0 363 2704
Biso mean---40.4 -
Num. residues----311
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.51820.34181390.2965302695
1.5182-1.53750.29821300.2835289195
1.5375-1.55770.26011380.2697299495
1.5577-1.5790.30761390.2575305796
1.579-1.60160.24581380.2538291795
1.6016-1.62550.24781430.2395308796
1.6255-1.65090.23971360.2316291396
1.6509-1.6780.22831410.2256305896
1.678-1.70690.21621400.2198300996
1.7069-1.73790.2461360.212303696
1.7379-1.77140.24441390.2162295896
1.7714-1.80750.261430.2128307596
1.8075-1.84680.2391380.2091294596
1.8468-1.88980.26311440.225308396
1.8898-1.9370.2091280.2056283893
1.937-1.98940.24541450.2054302996
1.9894-2.04790.18751460.1765306896
2.0479-2.1140.1781360.1803291695
2.114-2.18950.20971410.1735304996
2.1895-2.27720.24331320.1746278190
2.2772-2.38080.17861370.1678296295
2.3808-2.50630.23021390.1663302196
2.5063-2.66330.21221390.1619300396
2.6633-2.86880.19081390.158296795
2.8688-3.15730.22491420.1514301895
3.1573-3.61370.16871320.1423286392
3.6137-4.5510.16021330.1169286192
4.551-33.40.13981240.1473263784
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)
11.8210.4018-1.01281.4356-0.71772.30720.3379-1.36250.33470.4339-0.25270.0407-0.17940.6915-0.02780.3599-0.14470.02030.7021-0.15570.181510.444-10.93627.843
23.463-0.8747-2.30655.69111.61095.52870.7055-0.37811.4690.14740.15581.1617-0.8061-0.7063-0.21380.32430.02690.21070.3418-0.03510.5909-3.234-10.24825.563
34.81480.3382-4.06284.55881.2165.61460.62290.14750.8853-0.11240.18110.8735-0.4907-0.4781-0.6770.31940.00210.06590.1911-0.00790.3981-4.273-4.31724.498
42.9297-0.1569-1.03832.23660.971.98210.0092-0.0021-0.0763-0.1674-0.0148-0.1567-0.05130.1709-0.0050.11330.0157-0.01020.11960.03280.13438.46-9.4959.509
51.5076-0.11310.03661.98090.25621.63310.0011-0.0025-0.19770.0425-0.02330.00210.1380.06270.02760.10280.0042-0.0060.09650.02420.17319.087-26.276-0.81
62.00060.0198-0.18722.82850.91551.7472-0.0038-0.2213-0.37940.20570.0406-0.24210.2030.3245-0.06270.13270.0277-0.03540.19570.06070.217716.586-29.4226.324
71.74221.0085-0.81422.44120.97553.30620.5724-1.30540.62410.1407-0.2353-0.4179-0.50210.7753-0.21750.2549-0.1788-0.01010.5283-0.17640.207915.685-10.77618.273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 58:132 )A58 - 132
2X-RAY DIFFRACTION2( CHAIN A AND RESID 133:154 )A133 - 154
3X-RAY DIFFRACTION3( CHAIN A AND RESID 155:171 )A155 - 171
4X-RAY DIFFRACTION4( CHAIN A AND RESID 172:202 )A172 - 202
5X-RAY DIFFRACTION5( CHAIN A AND RESID 203:271 )A203 - 271
6X-RAY DIFFRACTION6( CHAIN A AND RESID 272:305 )A272 - 305
7X-RAY DIFFRACTION7( CHAIN A AND RESID 306:350 )A306 - 350

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