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- PDB-3w6m: Contribution of disulfide bond toward thermostability in hyperthe... -

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Basic information

Entry
Database: PDB / ID: 3w6m
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
458aa long hypothetical endo-1,4-beta-glucanase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 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 1.3Nov 6, 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)130,4439
Polymers129,8903
Non-polymers5536
Water15,799877
1
A: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3892
Polymers43,2971
Non-polymers921
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)43,7576
Polymers43,2971
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 458aa long hypothetical endo-1,4-beta-glucanase


Theoretical massNumber of molelcules
Total (without water)43,2971
Polymers43,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.236, 58.675, 138.539
Angle α, β, γ (deg.)90.000, 108.940, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-843-

HOH

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Components

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


Mass: 43296.648 Da / Num. of mol.: 3 / Fragment: UNP resideus 34-410 / Mutation: P74C
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 2.37 Å3/Da / Density % sol: 48.13 % / Mosaicity: 0.392 °
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: 1.948→50 Å / Num. obs: 88558 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.085 / Χ2: 1.196 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.984.10.30543171.006198.5
1.98-2.024.20.26843551.062198.5
2.02-2.064.20.23443531.096198.7
2.06-2.14.20.20843931.148199
2.1-2.154.20.19343691.152199.3
2.15-2.24.20.17444011.214198.8
2.2-2.254.20.15343901.227199.1
2.25-2.314.30.15243911.255199.4
2.31-2.384.30.13644291.189199.6
2.38-2.464.30.12444051.273199.5
2.46-2.544.30.11744101.239199.8
2.54-2.654.40.10744311.25199.6
2.65-2.774.40.09644571.229199.8
2.77-2.914.50.08644401.2631100
2.91-3.14.50.07644471.2281100
3.1-3.334.60.06844581.2391100
3.33-3.674.60.0644961.0821100
3.67-4.24.60.05244801.2351100
4.2-5.294.50.04645161.2241100
5.29-504.40.05246201.274199.6

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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: 1.948→34.534 Å / Occupancy max: 1 / Occupancy min: 0.67 / FOM work R set: 0.8975 / SU ML: 0.42 / σ(F): 1.35 / Phase error: 17.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 4453 5.03 %
Rwork0.1543 --
obs0.156 88537 99.04 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.388 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 71.26 Å2 / Biso mean: 15.6121 Å2 / Biso min: 3.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.0275 Å20 Å20.0426 Å2
2--0.0703 Å2-0 Å2
3----0.0979 Å2
Refinement stepCycle: LAST / Resolution: 1.948→34.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9201 0 36 877 10114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079564
X-RAY DIFFRACTIONf_angle_d1.08313038
X-RAY DIFFRACTIONf_chiral_restr0.081308
X-RAY DIFFRACTIONf_plane_restr0.0051662
X-RAY DIFFRACTIONf_dihedral_angle_d12.453357
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 (%)
1.9481-1.97020.2271060.15272365247185
1.9702-1.99340.2271530.1612763291699
1.9934-2.01770.1841490.15512810295999
2.0177-2.04320.20011530.14762748290199
2.0432-2.07010.2021280.14972785291399
2.0701-2.09840.21271520.14892798295099
2.0984-2.12840.20761480.15462778292699
2.1284-2.16020.19851530.15422803295699
2.1602-2.19390.20731600.14572752291299
2.1939-2.22990.17231520.1482750290299
2.2299-2.26830.19291510.14332833298499
2.2683-2.30960.21041270.151928282955100
2.3096-2.3540.18421510.155927962947100
2.354-2.4020.21181470.156727642911100
2.402-2.45420.17191510.153228452996100
2.4542-2.51130.19591210.153828362957100
2.5113-2.57410.1961510.160628152966100
2.5741-2.64370.22981630.166627892952100
2.6437-2.72140.21271380.159628242962100
2.7214-2.80920.19781470.159428232970100
2.8092-2.90960.18791600.160528252985100
2.9096-3.0260.21241530.160428372990100
3.026-3.16370.18111560.163928332989100
3.1637-3.33030.17671630.14928102973100
3.3303-3.53880.17531350.148828582993100
3.5388-3.81170.14961530.14528452998100
3.8117-4.19470.171550.133628713026100
4.1947-4.80030.14941490.133328593008100
4.8003-6.04260.17931820.164228743056100
6.0426-34.53940.21721460.200729673113100

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