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- PDB-8x3a: Solution NMR structure of cellulosomal double-dockerin module of ... -

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Basic information

Entry
Database: PDB / ID: 8x3a
TitleSolution NMR structure of cellulosomal double-dockerin module of Clo1313_0689 from Clostridium thermocellum
ComponentsSerine protease
KeywordsPROTEIN BINDING / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Subtilisin SUB1-like catalytic domain / : / Fervidolysin N-terminal prodomain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Peptidase S8, subtilisin, His-active site / : ...Subtilisin SUB1-like catalytic domain / : / Fervidolysin N-terminal prodomain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, C. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070125 China
CitationJournal: Protein Sci. / Year: 2024
Title: A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features.
Authors: Chen, C. / Yang, H. / Dong, S. / You, C. / Morais, S. / Bayer, E.A. / Liu, Y.J. / Xuan, J. / Cui, Q. / Mizrahi, I. / Feng, Y.
History
DepositionNov 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7885
Polymers16,6271
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine protease


Mass: 16627.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: cprA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2HPT9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-13C; U-15N] dDoc_0689, 50 mM sodium acetate, 50 mM potassium chloride, 10 mM CaCl2, 3 mg/L DTT, 0.02 % w/v DSS, 90% H2O/10% D2O
Label: sample1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMdDoc_0689[U-13C; U-15N]1
50 mMsodium acetatenatural abundance1
50 mMpotassium chloridenatural abundance1
10 mMCaCl2natural abundance1
3 mg/LDTTnatural abundance1
0.02 % w/vDSSnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: condition1 / pH: 4.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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