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- PDB-1cbh: DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE C-TERMINA... -

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Basic information

Entry
Database: PDB / ID: 1cbh
TitleDETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE C-TERMINAL DOMAIN OF CELLOBIOHYDROLASE I FROM TRICHODERMA REESEI. A STUDY USING NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
ComponentsC-TERMINAL DOMAIN OF CELLOBIOHYDROLASE I
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHypocrea jecorina (fungus)
MethodSOLUTION NMR
AuthorsClore, G.M. / Gronenborn, A.M.
CitationJournal: Biochemistry / Year: 1989
Title: Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance ...Title: Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.
Authors: Kraulis, J. / Clore, G.M. / Nilges, M. / Jones, T.A. / Pettersson, G. / Knowles, J. / Gronenborn, A.M.
History
DepositionMay 30, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-TERMINAL DOMAIN OF CELLOBIOHYDROLASE I


Theoretical massNumber of molelcules
Total (without water)3,7461
Polymers3,7461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide C-TERMINAL DOMAIN OF CELLOBIOHYDROLASE I


Mass: 3746.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus)
References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: XPLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M.NILGES, G.M.CLORE, A.M. GRONENBORN, ...Details: REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317-324 (1988)) USING THE PROGRAM XPLOR (A.T. BRUENGER, YALE UNIVERSITY, CT 06511). STRUCTURAL STATISTICS RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)* RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS) ALL 578 0.024 INTERRESIDUE SHORT RANGE 206 0.030 INTERRESIDUE LONG RANGE 137 0.017 INTRARESIDUE 211 0.021 HBOND *(2)* 24 0.019 POTENTIAL ENERGY TERMS TYPE ENERGY (KCAL/MOL) F(NOE) *(3)* 17 F(TOR) *(4)* 0 F(REPEL) *(5)* 34 LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS -118 KCAL/MOL. DEVIATIONS FROM IDEALIZED GEOMETRY *(6)* TYPE TOTAL NUMBER RMS DEVIATION BONDS 503 0.010 (ANGSTROMS) ANGLES 896 2.170 (DEGREES) IMPROPERS 227 0.911 (DEGREES) NOTES. *(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS ARE CALCULATED WITH RESPECT TO THE UPPER AND LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN 0.5 ANGSTROMS. *(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO RESTRAINTS - R(NH-O) .LT. 2.3 ANGSTROMS AND R(N-O) .LT. 3.3 ANGSTROMS. THE LOWER LIMITS ARE GIVEN BY THE SUM OF THE VAN DER WAALS RADII OF THE RELEVANT ATOMS. *(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL F(NOE) ARE CALCULATED WITH A FORCE CONSTANT OF 50 KCAL/MOL/ANGSTROM**2. *(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO RESTRICT THE RANGES OF 33 PHI ,24 PSI AND 25 CHI1 TORSION ANGLES. *(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF 4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY FUNCTION. *(6)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION OF PROLINES) IN THE TRANS CONFORMATION. IN THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS, THE RESTRAINTS FOR THE DISULFIDE BRIDGES ARE INCLUDED IN THE BOND AND ANGLE TERMS. A TOTAL OF 41 STRUCTURES CONSISTENT WITH THE NMR DATA WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THE 41 STRUCTURES ARE GIVEN IN THE PROTEIN DATA BANK ENTRY *2CBH*. THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS ARE AVAILABLE IN THE RESTRAINT FILE.
NMR ensembleConformers submitted total number: 1

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