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- PDB-5dhd: Crystal structure of ChBD2 from Thermococcus kodakarensis KOD1 -

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Basic information

Entry
Database: PDB / ID: 5dhd
TitleCrystal structure of ChBD2 from Thermococcus kodakarensis KOD1
ComponentsChitinase
KeywordsHYDROLASE / chitin / chitinase / chitin binding domain
Function / homology
Function and homology information


polysaccharide binding / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / extracellular region
Similarity search - Function
Immunoglobulin-like - #290 / Chitin-binding domain type 3 / Cellulose binding domain / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily ...Immunoglobulin-like - #290 / Chitin-binding domain type 3 / Cellulose binding domain / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PE3 / Chitinase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.27 Å
AuthorsHibi, M. / Niwa, S. / Takeda, K. / Miki, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
CREST, JST Japan
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structures of chitin binding domains of chitinase from Thermococcus kodakarensis KOD1
Authors: Hanazono, Y. / Takeda, K. / Niwa, S. / Hibi, M. / Takahashi, N. / Kanai, T. / Atomi, H. / Miki, K.
History
DepositionAug 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9329
Polymers10,9311
Non-polymers4,0018
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.245, 60.245, 68.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chitinase / Chitinase / containing dual catalytic domains


Mass: 10931.009 Da / Num. of mol.: 1 / Fragment: UNP residues 621-720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: Pk-chiA, TK1765 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UWR7, chitinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C28H58O15
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEGMME 5000, ammonium sulfate, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 36880 / % possible obs: 98.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.062 / Χ2: 1.637 / Net I/av σ(I): 39.2 / Net I/σ(I): 14.1 / Num. measured all: 264688
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.27-1.292.60.37715801.05686.6
1.29-1.323.60.4118191.10597.1
1.32-1.344.20.40418451.1299.3
1.34-1.374.70.38618421.19699.1
1.37-1.44.80.38318401.23599.2
1.4-1.435.20.35918691.35299.6
1.43-1.475.40.34218381.46299.6
1.47-1.515.80.30518521.6199.5
1.51-1.556.30.26618421.70899.7
1.55-1.66.80.22618531.91999.5
1.6-1.667.10.2118551.823100
1.66-1.727.50.17518791.92199.7
1.72-1.88.10.14318391.83899.9
1.8-1.98.70.12318771.81499.9
1.9-2.029.30.12118551.66599.8
2.02-2.179.80.13318761.75699.9
2.17-2.3910.20.13818651.76699.9
2.39-2.7410.40.10318751.65699.9
2.74-3.4510.90.04518771.47399.8
3.45-50110.0319021.66999.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CNS1.3refinement
DENZOdata collection
SCALEPACKdata scaling
MOLREP11.0.05phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DHE

5dhe


Resolution: 1.27→50 Å / FOM work R set: 0.8546 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.1946 1827 4.9 %
Rwork0.1954 35030 -
obs-36857 98.6 %
Solvent computationBsol: 62.8652 Å2
Displacement parametersBiso max: 70 Å2 / Biso mean: 21.7732 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.119 Å20 Å20 Å2
2--1.119 Å20 Å2
3----2.237 Å2
Refinement stepCycle: final / Resolution: 1.27→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 104 60 929
Biso mean--46.61 32.47 -
Num. residues----98
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.0951.5
X-RAY DIFFRACTIONc_scbond_it2.5342
X-RAY DIFFRACTIONc_mcangle_it3.5142
X-RAY DIFFRACTIONc_scangle_it3.9122.5
LS refinement shellResolution: 1.27→1.28 Å / Rfactor Rfree: 0.4048 / Rfactor Rwork: 0.371
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3so4.param
X-RAY DIFFRACTION4pe3.param

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