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- PDB-4dm1: Contribution of disulfide bond toward thermostability in hyperthe... -

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Basic information

Entry
Database: PDB / ID: 4dm1
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: 1.75 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 15, 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 1.2Oct 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
Water19,4921082
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
Components on special symmetry positions
IDModelComponents
11B-813-

HOH

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Components

#1: Protein 458aa long hypothetical endo-1,4-beta-glucanase / endoglucanase / cellulase / EGPh


Mass: 43290.621 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-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.: 1082 / 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 / Χ2: 3.896 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.813.20.434107472.841187.5
1.81-1.893.80.341122792.781100
1.89-1.973.80.264121923.0381100
1.97-2.073.80.186122733.0351100
2.07-2.23.80.142122673.2461100
2.2-2.383.80.117122673.6891100
2.38-2.613.80.093123213.7081100
2.61-2.993.80.073123484.2761100
2.99-3.773.80.053123805.0031100
3.77-503.80.043126216.929199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→44.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.296 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 6097 5 %RANDOM
Rwork0.1596 ---
obs0.1621 121183 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.43 Å2 / Biso mean: 25.6904 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å20.13 Å2
2---0.12 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9207 0 75 1082 10364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.029603
X-RAY DIFFRACTIONr_angle_refined_deg2.2761.9313119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96551128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07324.387465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.245151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0111527
X-RAY DIFFRACTIONr_chiral_restr0.1790.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217509
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 356 -
Rwork0.242 6713 -
all-7069 -
obs--79.62 %

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