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- PDB-3w6l: Contribution of disulfide bond toward thermostability in hyperthe... -

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Basic information

Entry
Database: PDB / ID: 3w6l
TitleContribution of disulfide bond toward thermostability in hyperthermostable endocellulase
Components458aa long hypothetical endo-1,4-beta-glucanase
KeywordsHYDROLASE / Hyperthermophilic / Disulfide bond / TIM barrel / Glycosyl Hydrolase / Hydrolizaiton / Membrane-bound
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
CGP-CTERM domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 458aa long hypothetical endo-1,4-beta-glucanase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsKim, H.-W. / Ishikawa, K.
CitationJournal: Extremophiles / Year: 2013
Title: The role of disulfide bond in hyperthermophilic endocellulase
Authors: Kim, H.-W. / Ishikawa, K.
History
DepositionFeb 15, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 458aa long hypothetical endo-1,4-beta-glucanase
B: 458aa long hypothetical endo-1,4-beta-glucanase
C: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,29618
Polymers129,8723
Non-polymers1,42515
Water13,331740
1
A: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6715
Polymers43,2911
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0509
Polymers43,2911
Non-polymers7608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5764
Polymers43,2911
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.103, 58.340, 137.915
Angle α, β, γ (deg.)90.000, 109.650, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 458aa long hypothetical endo-1,4-beta-glucanase


Mass: 43290.621 Da / Num. of mol.: 3 / Fragment: UNP resideus 34-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1171 / Production host: Escherichia coli (E. coli) / References: UniProt: O58925, cellulase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M ammonium phosphate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 121695 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→37.527 Å / Occupancy max: 1 / Occupancy min: 0.62 / FOM work R set: 0.873 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 6096 5.03 %
Rwork0.1762 --
obs0.1777 121175 98.2 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.518 Å2 / ksol: 0.422 e/Å3
Displacement parametersBiso max: 65.31 Å2 / Biso mean: 23.9883 Å2 / Biso min: 9.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.3684 Å2-0 Å20.325 Å2
2---0.2756 Å20 Å2
3----0.0929 Å2
Refinement stepCycle: LAST / Resolution: 1.751→37.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9207 0 75 740 10022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079603
X-RAY DIFFRACTIONf_angle_d1.07213113
X-RAY DIFFRACTIONf_chiral_restr0.0791308
X-RAY DIFFRACTIONf_plane_restr0.0051665
X-RAY DIFFRACTIONf_dihedral_angle_d11.3823351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7506-1.77050.31581140.27392262237657
1.7705-1.79130.27092080.247538154023100
1.7913-1.81310.25662100.231638904100100
1.8131-1.83610.25712130.223738624075100
1.8361-1.86020.25812090.215338564065100
1.8602-1.88570.23131830.204539364119100
1.8857-1.91270.23661900.208338634053100
1.9127-1.94120.2522020.202739114113100
1.9412-1.97150.23722260.202438244050100
1.9715-2.00390.23392160.193439314147100
2.0039-2.03840.22752120.185537994011100
2.0384-2.07550.21091920.177239214113100
2.0755-2.11540.21342020.171438924094100
2.1154-2.15860.20072090.178139034112100
2.1586-2.20550.21342130.17438724085100
2.2055-2.25680.19021950.172139294124100
2.2568-2.31320.22751960.184338444040100
2.3132-2.37580.2322110.184338914102100
2.3758-2.44560.21932060.181639224128100
2.4456-2.52460.22062130.182838714084100
2.5246-2.61480.21762230.177138814104100
2.6148-2.71940.192040.172339294133100
2.7194-2.84320.192110.165738624073100
2.8432-2.9930.18651930.166839404133100
2.993-3.18040.18852040.165738894093100
3.1804-3.42580.18952090.1593928413799
3.4258-3.77030.17641960.15683884408099
3.7703-4.31520.17292020.14683911411399
4.3152-5.43410.18812120.1593918413098
5.4341-37.53530.21082220.20643943416597

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