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- PDB-1cx1: SECOND N-TERMINAL CELLULOSE-BINDING DOMAIN FROM CELLULOMONAS FIMI... -

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Basic information

Entry
Database: PDB / ID: 1cx1
TitleSECOND N-TERMINAL CELLULOSE-BINDING DOMAIN FROM CELLULOMONAS FIMI BETA-1,4-GLUCANASE C, NMR, 22 STRUCTURES
ComponentsENDOGLUCANASE C
KeywordsHYDROLASE / CELLULOSE-BINDING DOMAIN / CELLOOLIGOSACHARIDES / CELLULASE / PROTEIN- CARBOHYDRATE INTERACTION
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycoside hydrolase family 9 ...Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding domain-like / Immunoglobulin I-set / Immunoglobulin I-set domain / Galactose-binding-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin E-set / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCellulomonas fimi (bacteria)
MethodSOLUTION NMR / ALL CALCULATIONS WERE PERFORMED USING X-PLOR V3.8 WITH SCRIPTS FROM THE X-PLOR 3.1 MANUAL A. A. BRUNGER (1992), NEW HAVEN: YALE UNIVERSITY PRESS ACCORDING TO THE METHOD DESCRIBED BY M. NILGES, G. M. CLORE, A. M. GRONENBORN
Model type detailsminimized average
AuthorsBrun, E. / Johnson, P.E. / Creagh, L.A. / Haynes, C.A. / Tomme, P. / Webster, P. / Kilburn, D.G. / McIntosh, L.P.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C.
Authors: Brun, E. / Johnson, P.E. / Creagh, A.L. / Tomme, P. / Webster, P. / Haynes, C.A. / McIntosh, L.P.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The cellulose-binding domains from Cellulomonas fimi beta-1, 4-glucanase CenC bind nitroxide spin-labeled cellooligosaccharides in multiple orientations
Authors: Brun, E. / Johnson, P.E. / MacKenzie, L. / Withers, S.G. / McIntosh, L.P.
#2: Journal: Biochemistry / Year: 1997
Title: Structure of the N-terminal Cellulose-Binding Domain of Cellulomonas Fimi CenC Determined by Nucelar Magnetic Resonance Spectroscopy
Authors: Johnson, P.E. / Joshi, M.D. / Tomme, P. / Kilburn, D.G. / McIntosh, L.P.
History
DepositionAug 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE C


Theoretical massNumber of molelcules
Total (without water)15,8771
Polymers15,8771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 60STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #22minimized average structure

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Components

#1: Protein ENDOGLUCANASE C


Mass: 15877.379 Da / Num. of mol.: 1 / Fragment: RESIDUES 176-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P14090, cellulase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1223D 15N-SEPARATED NOESY
1332D NOESY
1414D 13C/15N-SEPARATED NOESY
152HNHA
NMR detailsText: CBDN2 WAS STUDIED IN THE PRESENCE OF SATURATING CONCENTRATIONS OF CELLOPENTAOSE. HOWEVER, DUE TO SPECTRAL OVERLAP, THE OLIGOSACCHARIDE WAS NOT INCLUDED IN THE STRUCTURE CALCULATIONS

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Sample preparation

Details
Solution-IDContents
11.5 TO 2 MM CBDN2 U-15N, 13C; UP TO 22-FOLD MOLAR EXCESS OF CELLOPENTAOSE; IN 50 MM NACL, 50 MM PHOSPHATE BUFFER K AT PH* 6.5,
21.5 TO 2 MM CBDN2 U-15N; UP TO 22-FOLD MOLAR EXCESS OF CELLOPENTAOSE; IN 50 MM NACL, 50 MM PHOSPHATE BUFFER K AT PH* 6.5,
31.5 TO 2 MM CBDN2 UNLABELED; UP TO 22-FOLD MOLAR EXCESS OF CELLOPENTAOSE; IN 50 MM NACL, 50 MM PHOSPHATE BUFFER K AT PH* 6.5,
Sample conditionsIonic strength: 50mMNACL / pH: 6 / Pressure: 1 atm / Temperature: 35 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Acollection
Felix230processing
Felix230data analysis
X-PLOR3.8structure solution
X-PLOR3.8BRUNGER, A. ET AL.refinement
RefinementMethod: ALL CALCULATIONS WERE PERFORMED USING X-PLOR V3.8 WITH SCRIPTS FROM THE X-PLOR 3.1 MANUAL A. A. BRUNGER (1992), NEW HAVEN: YALE UNIVERSITY PRESS ACCORDING TO THE METHOD DESCRIBED BY M. ...Method: ALL CALCULATIONS WERE PERFORMED USING X-PLOR V3.8 WITH SCRIPTS FROM THE X-PLOR 3.1 MANUAL A. A. BRUNGER (1992), NEW HAVEN: YALE UNIVERSITY PRESS ACCORDING TO THE METHOD DESCRIBED BY M. NILGES, G. M. CLORE, A. M. GRONENBORN
Software ordinal: 1
Details: A TOTAL OF 1510 NOE DERIVED DISTANCE RESTRAINTS THAT COMPRISE 700 INTRARESIDUE, 332 SEQUENTIAL, 83 SHORT RANGE (1<|I-J|<=4), 394 LONG RANGE (|I-J|>4) WERE INCLUDED.. 1 DISULPHIDE BOND DISTANCE RESTRAINT, 86 HYDROGEN BOND RESTRAINTS, 53 PHI ANGLE RESTRAINTS, 70 PSI ANGLE RESTRAINTS, AND 48 CHI1 RESTRAINTS WERE ALSO INCLUDED.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 60 / Conformers submitted total number: 22

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