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- PDB-5dhe: Crystal structure of ChBD3 from Thermococcus kodakarensis KOD1 -

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Basic information

Entry
Database: PDB / ID: 5dhe
TitleCrystal structure of ChBD3 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
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsNiwa, S. / Hibi, M. / 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 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4777
Polymers22,0162
Non-polymers4605
Water3,495194
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2844
Polymers11,0081
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-1 kcal/mol
Surface area5460 Å2
MethodPISA
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1923
Polymers11,0081
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.161, 44.669, 51.712
Angle α, β, γ (deg.)90.000, 114.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11008.195 Da / Num. of mol.: 2 / Fragment: ChBD3 domain, UNP residues 764-863
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: sodium citrate, glycerol, MES, SDS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 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: 0.9 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Number: 123739 / Rmerge(I) obs: 0.085 / Χ2: 1.6 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 31247 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.515010.0341.4973.9
5.176.5110.0391.3964
4.525.1710.0361.4154
4.14.5210.041.4914
3.814.110.0491.5984
3.583.8110.0551.6114
3.413.5810.0651.7634
3.263.4110.0731.7634
3.133.2610.091.7264
3.023.1310.1161.7664
2.933.0210.1371.6394
2.852.9310.1571.6564
2.772.8510.1811.6534
2.72.7710.1711.6044
2.642.710.2061.6234
2.592.6410.2461.6014
2.532.5910.2611.5714
2.492.5310.2671.5883.9
2.442.4910.3131.5533.9
2.42.4410.2981.4713.9
ReflectionResolution: 1.6→30 Å / Num. obs: 26632 / % possible obs: 98.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.061 / Χ2: 1.869 / Net I/av σ(I): 28.806 / Net I/σ(I): 13.6 / Num. measured all: 107174
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.632.90.37411781.56588.2
1.63-1.663.10.35912481.62792.9
1.66-1.693.60.35812941.66197.8
1.69-1.724.10.31813311.73199.9
1.72-1.764.10.25513451.73100
1.76-1.84.20.21613381.691100
1.8-1.854.10.18213401.868100
1.85-1.94.20.15613351.897100
1.9-1.954.20.13413491.895100
1.95-2.024.20.10913311.954100
2.02-2.094.20.09413341.897100
2.09-2.174.20.08913322.04100
2.17-2.274.20.07813592.24100
2.27-2.394.20.07613242.344100
2.39-2.544.20.06513522.103100
2.54-2.744.20.05113761.794100
2.74-3.014.20.0513462.083100
3.01-3.454.10.04213552.364100
3.45-4.344.20.02813591.46599.9
4.34-3040.02314061.16399.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3 Å / D res low: 15 Å / FOM : 0.39 / Reflection: 7742
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Os29.6490.999010.317
2Os23.3230.8690.7260.9990.298
3Os29.8650.5450.5230.3290.338
4Os31.040.4190.80.3260.321
Phasing MAD shell
Resolution (Å)FOM Reflection
9.2-150.51445
6.36-9.20.51666
5.13-6.360.45820
4.42-5.130.44962
3.94-4.420.41086
3.58-3.940.371183
3.31-3.580.321250
3.09-3.310.261330

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Processing

Software
NameVersionClassification
CNS1.3refinement
DENZOdata collection
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.6→30 Å / FOM work R set: 0.8763 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2093 1339 5 %
Rwork0.1935 25280 -
obs-26619 98.5 %
Solvent computationBsol: 44.2818 Å2
Displacement parametersBiso max: 51.52 Å2 / Biso mean: 14.7357 Å2 / Biso min: 1.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.175 Å20 Å2-0.954 Å2
2---1.504 Å20 Å2
3---0.328 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 30 194 1786
Biso mean--39.72 28.05 -
Num. residues----200
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3gol.param

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