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- PDB-1gzj: Structure of Thermoascus aurantiacus family 5 endoglucanase -

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Basic information

Entry
Database: PDB / ID: 1gzj
TitleStructure of Thermoascus aurantiacus family 5 endoglucanase
ComponentsEGI
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 5
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 / MIRAS / Resolution: 1.62 Å
AuthorsLo Leggio, L. / Pickersgill, R.W. / Larsen, S.
Citation
Journal: FEBS Lett. / Year: 2002
Title: The 1.62 A Structure of Thermoascus Aurantiacus Endoglucanase: Completing the Structural Picture of Subfamilies in Glycoside Hydrolase Family 5
Authors: Lo Leggio, L. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminaryx-Ray Analysis of the Major Endoglucanase from Thermoascus Aurantiacus
Authors: Loleggio, L. / Parry, N.J. / Van Beeumen, J. / Claeyssens, M. / Bhat, M.W. / Pickersgill, R.W.
History
DepositionMay 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_nat / struct_ref / struct_ref_seq
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 9-STRANDED BARRELS THESE ARE REPRESENTED BY A 10-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: EGI
B: EGI


Theoretical massNumber of molelcules
Total (without water)67,3172
Polymers67,3172
Non-polymers00
Water7,008389
1
A: EGI


Theoretical massNumber of molelcules
Total (without water)33,6581
Polymers33,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EGI


Theoretical massNumber of molelcules
Total (without water)33,6581
Polymers33,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.510, 85.850, 89.640
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: (-0.98219, 0.17473, 0.069144), (0.17639, 0.98414, 0.018609), (-0.64797, 0.30474, -0.99743)
Vector: 38.002, -4.092, 42.089)

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Components

#1: Protein EGI / Endoglucanase / ENDO TYPE CELLULASE ENGI


Mass: 33658.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermoascus aurantiacus (fungus) / References: UniProt: Q8TG26, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.75 %
Description: DUE TO LOW COMPLETENESS AT LOW RESOLUTION, THE MISSING LOW RESOLUTION REFLECTIONS WERE 'REFILLED' WITH DATA FROM AN IN HOUSE COLLECTION AFTER THE TWO DATA SETS WERE SCALED TOGETHER. THE ...Description: DUE TO LOW COMPLETENESS AT LOW RESOLUTION, THE MISSING LOW RESOLUTION REFLECTIONS WERE 'REFILLED' WITH DATA FROM AN IN HOUSE COLLECTION AFTER THE TWO DATA SETS WERE SCALED TOGETHER. THE STATISTICS REPORTED REFER TO THE SYNCHROTRON DATA SET. AFTER REFILLING THE OVERALL COMPLETENESS WAS 88.5% (99.2% BETWEEN 35 AND 5 A RESOLUTION)
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP CONSISTING OF 2 UL OF PROTEIN (31.2 MG/ML) AND 2 UL RESERVOIR (0.1 M TRIS-HCL PH9.0, 1.6 M AMMONIUM SULPHATE), pH 9.00
Crystal grow
*PLUS
Temperature: 291 K / pH: 8.5 / Method: vapor diffusion, hanging drop
Details: Loleggio, L., (1997) Acta Crystallogr.,Sect.D, 53, 599.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112.3 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH8.5
32.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→35.35 Å / Num. obs: 60922 / % possible obs: 81.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.289 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
SHARPphasing
ARPphasing
DMphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.62→34.94 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2374111.56 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.177 6796 10.1 %RANDOM
Rwork0.159 ---
obs0.159 67019 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3663 Å2 / ksol: 0.328418 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å20 Å2
2---1.16 Å20 Å2
3----1.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.62→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4746 0 0 389 5135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 1062 10.3 %
Rwork0.193 9295 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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