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- PDB-1tml: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF A THERMOPHILIC ENDOC... -

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Basic information

Entry
Database: PDB / ID: 1tml
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF A THERMOPHILIC ENDOCELLULASE
ComponentsENDO-1,4-BETA-D-GLUCANASE
KeywordsBETA-AMYLASE / ENDOCELLULASE / CATALYTIC DOMAIN
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide binding / cellulose catabolic process
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / Cellulose binding domain ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSpezio, M. / Wilson, D.B. / Karplus, P.A.
Citation
Journal: Biochemistry / Year: 1993
Title: Crystal structure of the catalytic domain of a thermophilic endocellulase.
Authors: Spezio, M. / Wilson, D.B. / Karplus, P.A.
#1: Journal: To be Published
Title: Crystal Structure of the Catalytic Domain of a Thermophilic Endocellulase
Authors: Spezio, M. / Wilson, D.B. / Karplus, P.A.
History
DepositionJun 8, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEET PRESENTED AS *COR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *COR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. IN ADDITION, STRAND 1 IS BIFURCATED THUS THE BARREL IS REPRESENTED BY TWO SETS OF SHEET RECORDS *COR* AND *BOR* WHERE STRANDS 2, 3, 4, 5, 6, 7, AND 8 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-BETA-D-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5332
Polymers30,4371
Non-polymers961
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.350, 65.940, 43.410
Angle α, β, γ (deg.)90.00, 107.69, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES ASN 1 AND ASP 2 ARE NOT WELL ORDERED AND HAVE VERY WEAK ELECTRON DENSITY.
2: RESIDUE TRP 162, IN THE ACTIVE SITE CLEFT, IS WELL ORDERED AND HAS STRONG DENSITY EVEN THOUGH ITS MAIN CHAIN TORSION ANGLES ARE OUTSIDE THE FAVORABLE REGIONS OF A RAMACHANDRAN PLOT.

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Components

#1: Protein ENDO-1,4-BETA-D-GLUCANASE


Mass: 30436.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / References: UniProt: P26222, cellulase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Compound detailsD1 AND F1 OF THE HELIX ARE SMALL AND ARE NOT EXACTLY CONSERVED BETWEEN THIS STRUCTURE AND ...D1 AND F1 OF THE HELIX ARE SMALL AND ARE NOT EXACTLY CONSERVED BETWEEN THIS STRUCTURE AND CELLOBIOHYDROLASE II.
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: GUN2_THEFU SWISS-PROT RESIDUE PDB ATOM RECORDS NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 162 TRP 162 ASP 163 HIS 163 GLN 166 ALA 166

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.62 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-18 mg/mlprotein1drop
22 mMMES1drop
30.04 %(w/v)1dropNaN3
40.0056 Mdisodium citrate1reservoir
510 mM1reservoirCaCl2
612 %ammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 21081 / % possible obs: 97 % / Num. measured all: 79576 / Rmerge(I) obs: 0.0459

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.184 / Rfactor obs: 0.184 / Highest resolution: 1.8 Å
Details: RESIDUES ASN 1 AND ASP 2 ARE NOT WELL ORDERED AND HAVE VERY WEAK ELECTRON DENSITY. RESIDUE TRP 162, IN THE ACTIVE SITE CLEFT, IS WELL ORDERED AND HAS STRONG DENSITY EVEN THOUGH ITS MAIN ...Details: RESIDUES ASN 1 AND ASP 2 ARE NOT WELL ORDERED AND HAVE VERY WEAK ELECTRON DENSITY. RESIDUE TRP 162, IN THE ACTIVE SITE CLEFT, IS WELL ORDERED AND HAS STRONG DENSITY EVEN THOUGH ITS MAIN CHAIN TORSION ANGLES ARE OUTSIDE THE FAVORABLE REGIONS OF A RAMACHANDRAN PLOT.
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 5 219 2843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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