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- PDB-1dav: SOLUTION STRUCTURE OF THE TYPE I DOCKERIN DOMAIN FROM THE CLOSTRI... -

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Basic information

Entry
Database: PDB / ID: 1dav
TitleSOLUTION STRUCTURE OF THE TYPE I DOCKERIN DOMAIN FROM THE CLOSTRIDIUM THERMOCELLUM CELLULOSOME (20 STRUCTURES)
ComponentsENDOGLUCANASE SS
KeywordsHYDROLASE / CELLULOSE DEGRADATION / CELLULOSOME / CALCIUM-BINDING
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (reducing end) / cellulose 1,4-beta-cellobiosidase activity (reducing end) / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Type 1 dockerin domain / Dockerin domain / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain ...Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Type 1 dockerin domain / Dockerin domain / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cellulose 1,4-beta-cellobiosidase (reducing end) CelS / Cellulose 1,4-beta-cellobiosidase (reducing end) CelS
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLytle, B.L. / Volkman, B.F. / Westler, W.M. / Heckman, M.P. / Wu, J.H.D.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain.
Authors: Lytle, B.L. / Volkman, B.F. / Westler, W.M. / Heckman, M.P. / Wu, J.H.D.
#1: Journal: ARCH.BIOCHEM.BIOPHYS. / Year: 2000
Title: Secondary Structure and Calcium-induced Folding of the Clostridium thermocellum Dockerin Domain Determined by NMR Spectroscopy
Authors: Lytle, B.L. / Volkman, B.F. / Westler, W.M. / Wu, J.H.D.
#2: Journal: J.Bacteriol. / Year: 1998
Title: Involvement of Both Dockerin Subdomains in Assembly of the Clostridium thermocellum Cellulosome
Authors: Lytle, B. / Wu, J.H.D.
History
DepositionOct 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650 HELIX DETERMINATION METHOD: AUTHOR-DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9393
Polymers7,8591
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
Representative

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Components

#1: Protein ENDOGLUCANASE SS / CELS


Mass: 7858.770 Da / Num. of mol.: 1 / Fragment: TYPE I DOCKERIN DOMAIN (RESIDUES 673-741)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Plasmid: PCYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3)
References: UniProt: P38686, UniProt: P0C2S5*PLUS, cellulase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1212D NOESY
2322D NOESY
2413D 15N-SEPARATED TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED BY STANDARD TECHNIQUES USING UNLABELED AND 15N- LABELED DOCKERIN.

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Sample preparation

DetailsContents: 100MM POTASSIUM CHLORIDE; 20MM CALCIUM CHLORIDE; 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM KCL 61 atm328 K
2100mM KCL 61 atm328 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5P.GUENTERT, C.MUMENTHALER, K.WUETHRICHrefinement
DYANA1.5P.GUENTERT, C.MUMENTHALER, K.WUETHRICHstructure solution
Felix95MOLECULAR SIMULATIONSprocessing
NMRPipeF. DELAGALIO, S. GRZESIEK, G. VUISTER, G. ZHU, J. PFEIFER, A. BAXprocessing
XEASY1.2structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON 728 NOE-DERIVED DISTANCE CONSTRAINTS, 79 DIHEDRAL ANGLE CONSTRAINTS, AND 12 CALCIUM ION RESTRAINTS.
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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