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- PDB-1h1n: Atomic resolution structure of the major endoglucanase from Therm... -

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Basic information

Entry
Database: PDB / ID: 1h1n
TitleAtomic resolution structure of the major endoglucanase from Thermoascus aurantiacus
ComponentsENDO TYPE CELLULASE ENGI
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / FAMILY 5 / SUBTYPE / THERMOPHILIC / THERMOPHILE / ENDOGLUCANASE
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesTHERMOASCUS AURANTIACUS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.12 Å
AuthorsVan Petegem, F. / Vandenberghe, I. / Bhat, M.K. / Van Beeumen, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Atomic Resolution Structure of the Major Endoglucanase from Thermoascus Aurantiacus
Authors: Van Petegem, F. / Vandenberghe, I. / Bhat, M.K. / Van Beeumen, J.
History
DepositionJul 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO TYPE CELLULASE ENGI
B: ENDO TYPE CELLULASE ENGI


Theoretical massNumber of molelcules
Total (without water)67,4632
Polymers67,4632
Non-polymers00
Water17,583976
1
A: ENDO TYPE CELLULASE ENGI


Theoretical massNumber of molelcules
Total (without water)33,7311
Polymers33,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDO TYPE CELLULASE ENGI


Theoretical massNumber of molelcules
Total (without water)33,7311
Polymers33,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.764, 84.728, 89.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.976, 0.203, -0.078), (-0.204, 0.979, -0.015), (0.074, 0.03, 0.997)
Vector: -44.93715, -29.14475, -6.83722)

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Components

#1: Protein ENDO TYPE CELLULASE ENGI / ENDO-1 / 4-GLUCANASE


Mass: 33731.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOASCUS AURANTIACUS (fungus) / Strain: IMI216529 / References: UniProt: Q8TG26, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 976 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SWISSPROT ENTRY Q8TG26 REPRESENTS THE SEQUENCE FROM THERMOASCUS AURANTIACUS STRAIN IF09748. THE ...THE SWISSPROT ENTRY Q8TG26 REPRESENTS THE SEQUENCE FROM THERMOASCUS AURANTIACUS STRAIN IF09748. THE CONFLICTS IN THE SEQUENCE ARE MOST LIKELY DUE TO THE VARIATION OBSERVED IN THE STRAIN (IMI216529) USED FOR THE CRYSTALLOGRAPHIC STUDY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 41.97 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Method: other
Details: Bhat, M.K., (2001) American Chemical Society, Washington DC, 204.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.12→15 Å / Num. obs: 232102 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 34.29
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.57 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 2988510
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.438

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
ARP/wARPphasing
SHELXL-97refinement
RefinementMethod to determine structure: SIR / Resolution: 1.12→15 Å / Num. parameters: 51673 / Num. restraintsaints: 61948 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.171 10835 5.2 %RANDOM
all0.1327 206423 --
obs0.1437 -94.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 4438 / Occupancy sum non hydrogen: 5697
Refinement stepCycle: LAST / Resolution: 1.12→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 0 976 5697
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0292
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.06
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.028
X-RAY DIFFRACTIONs_approx_iso_adps0.113
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.171 / Rfactor Rwork: 0.1093
Solvent computation
*PLUS
Displacement parameters
*PLUS

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