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- PDB-4dm2: Contribution of disulfide bond toward thermostability in hyperthe... -

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Basic information

Entry
Database: PDB / ID: 4dm2
TitleContribution of disulfide bond toward thermostability in hyperthermostable endocellulase
Components458aa long hypothetical endo-1,4-beta-glucanase
KeywordsHYDROLASE / TIM barrel / Glycosyl hydrolase / 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: 1.95 Å
AuthorsKim, H.-W. / Ishikawa, K.
CitationJournal: To be Published
Title: Contribution of disulfide bond toward thermostability in hyperthermostable endocellulase
Authors: Kim, H.-W. / Ishikawa, K.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 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

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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
Water5,999333
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, 108.930, 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 / Glycosyl Hydrolase / cellulase / endoglucanase /


Mass: 43296.648 Da / Num. of mol.: 3 / Fragment: UNP residues 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-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.: 333 / 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 %
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: 89041 / % possible obs: 99.5 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→34.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.857 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 4453 5 %RANDOM
Rwork0.1661 ---
obs0.1681 88548 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.94 Å2 / Biso mean: 14.4759 Å2 / Biso min: 2.99 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9201 0 36 333 9570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.029564
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.92413044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67351128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50424.387465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.853151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4021527
X-RAY DIFFRACTIONr_chiral_restr0.1690.21314
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217497
LS refinement shellResolution: 1.948→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 278 -
Rwork0.172 5490 -
all-5768 -
obs--91.12 %

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