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- PDB-2rtt: Solution structure of the chitin-binding domain of Chi18aC from S... -

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Basic information

Entry
Database: PDB / ID: 2rtt
TitleSolution structure of the chitin-binding domain of Chi18aC from Streptomyces coelicolor
ComponentsChiC
KeywordsHYDROLASE / chitin-binding domain / chitinase
Function / homology
Function and homology information


polysaccharide binding / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Immunoglobulin-like - #290 / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site ...Immunoglobulin-like - #290 / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailstarget function, model1
AuthorsOkumura, A. / Uemura, M. / Yamada, N. / Chikaishi, E. / Takai, T. / Yoshio, S. / Akagi, K. / Morita, J. / Lee, Y. / Yokogawa, D. ...Okumura, A. / Uemura, M. / Yamada, N. / Chikaishi, E. / Takai, T. / Yoshio, S. / Akagi, K. / Morita, J. / Lee, Y. / Yokogawa, D. / Suzuki, K. / Watanabe, T. / Ikegami, T.
CitationJournal: To be Published
Title: Solution structure of the Chitin-binding domain of chitinase Chi18aC from Streptomyces coelicolor
Authors: Okumura, A. / Uemura, M. / Yamada, N. / Chikaishi, E. / Takai, T. / Yoshio, S. / Akagi, K. / Morita, J. / Lee, Y. / Yokogawa, D. / Suzuki, K. / Watanabe, T. / Ikegami, T.
History
DepositionAug 26, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ChiC


Theoretical massNumber of molelcules
Total (without water)10,6091
Polymers10,6091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein ChiC / Chi18aC


Mass: 10609.293 Da / Num. of mol.: 1 / Fragment: UNP residues 31-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: chiC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z9M8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HNCO
1623D HN(CA)CO
1723D HBHA(CO)NH
1813D 1H-15N TOCSY
1922D 1H-13C HSQC
11012D 1H-15N HSQC
11123D C(CO)NH
11223D H(CCO)NH
11313D 1H-15N NOESY
11413D 1H-15N NOESY
11552D DQF-COSY
11652D 1H-1H NOESY
11733D 1H-15N NOESY
11823D 1H-13C NOESY
11932D 1H-15N HSQC
12033D 1H-13C NOESY aromatic
12124D H(CCO)NH
12233D (H)CCH-TOCSY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-15N] Chi18aC_CBD-1, 20 mM potassium phosphate-2, 0.02 % sodium azide-3, 1 mM DTT-4, 90 % H2O-5, 10 % [U-2H] D2O-6, 90% H2O/10% D2O90% H2O/10% D2O
20.64 mM [U-13C; U-15N] Chi18aC_CBD-7, 20 mM potassium phosphate-8, 0.02 % sodium azide-9, 1 mM DTT-10, 90 % H2O-11, 10 % [U-2H] D2O-12, 90% H2O/10% D2O90% H2O/10% D2O
30.71 mM [U-13C; U-15N] Chi18aC_CBD-13, 20 mM potassium phosphate-14, 0.02 % sodium azide-15, 1 mM DTT-16, 100 % [U-2H] D2O-17, 100% D2O100% D2O
40.37 mM [U-15% 13C; U-15N] Chi18aC_CBD-18, 20 mM potassium phosphate-19, 0.02 % sodium azide-20, 1 mM DTT-21, 90 % H2O-22, 10 % [U-2H] D2O-23, 90% H2O/10% D2O90% H2O/10% D2O
51.0 mM Chi18aC_CBD-24, 20 mM potassium phosphate-25, 0.02 % sodium azide-26, 1 mM DTT-27, 90 % H2O-28, 10 % [U-2H] D2O-29, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMChi18aC_CBD-1[U-15N]1
20 mMpotassium phosphate-21
0.02 %sodium azide-31
1 mMDTT-41
90 %H2O-51
10 %D2O-6[U-2H]1
0.64 mMChi18aC_CBD-7[U-13C; U-15N]2
20 mMpotassium phosphate-82
0.02 %sodium azide-92
1 mMDTT-102
90 %H2O-112
10 %D2O-12[U-2H]2
0.71 mMChi18aC_CBD-13[U-13C; U-15N]3
20 mMpotassium phosphate-143
0.02 %sodium azide-153
1 mMDTT-163
100 %D2O-17[U-2H]3
0.37 mMChi18aC_CBD-18[U-15% 13C; U-15N]4
20 mMpotassium phosphate-194
0.02 %sodium azide-204
1 mMDTT-214
90 %H2O-224
10 %D2O-23[U-2H]4
1.0 mMChi18aC_CBD-245
20 mMpotassium phosphate-255
0.02 %sodium azide-265
1 mMDTT-275
90 %H2O-285
10 %D2O-29[U-2H]5
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003
Bruker AvanceBrukerAVANCE4004

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 30 / Representative conformer: 1

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