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- PDB-4dws: Crystal Structure of a chitinase from the Yersinia entomophaga to... -

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Basic information

Entry
Database: PDB / ID: 4dws
TitleCrystal Structure of a chitinase from the Yersinia entomophaga toxin complex
Components(Chi2) x 4
KeywordsSUGAR BINDING PROTEIN / TIM barrel / Chitinase / Reductive methylation
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #10 / 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 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily ...Chitinase A; domain 3 - #10 / 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 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesYersinia entomophaga (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBusby, J.N. / Hurst, M.R.H. / Lott, J.S.
CitationJournal: Nature / Year: 2013
Title: The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device.
Authors: Busby, J.N. / Panjikar, S. / Landsberg, M.J. / Hurst, M.R. / Lott, J.S.
History
DepositionFeb 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Chi2
B: Chi2
C: Chi2
D: Chi2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,6548
Polymers241,2854
Non-polymers3684
Water21,7261206
1
A: Chi2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4822
Polymers60,3891
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chi2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4132
Polymers60,3211
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chi2


Theoretical massNumber of molelcules
Total (without water)60,3611
Polymers60,3611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chi2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3973
Polymers60,2131
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.505, 210.556, 92.584
Angle α, β, γ (deg.)90.000, 95.270, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 4 biological units in the asymmetric unit (chains A, B, C and D).

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Chi2


Mass: 60389.480 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia entomophaga (bacteria) / Strain: MH96 / Gene: chi2 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A879
#2: Protein Chi2


Mass: 60321.371 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia entomophaga (bacteria) / Strain: MH96 / Gene: chi2 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A879
#3: Protein Chi2


Mass: 60361.434 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia entomophaga (bacteria) / Strain: MH96 / Gene: chi2 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A879
#4: Protein Chi2


Mass: 60213.184 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia entomophaga (bacteria) / Strain: MH96 / Gene: chi2 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A879

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Non-polymers , 2 types, 1210 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG 3350, 2% isopropanol, 0.1 M calcium chloride, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.8→105.278 Å / Num. all: 212127 / Num. obs: 212127 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rsym value: 0.115 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.97.20.5821.2224369309990.582100
1.9-2.017.50.3691.9219146293120.369100
2.01-2.157.60.2422.9209636275230.242100
2.15-2.327.70.1694.3196393256150.169100
2.32-2.557.70.1315.6181242235690.131100
2.55-2.857.70.17.3164504213460.1100
2.85-3.297.70.0858145177188300.085100
3.29-4.027.70.0679.8122447159500.067100
4.02-5.697.70.04614.194381123290.046100
5.69-19.8967.80.03817.25191066540.03897.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å19.9 Å
Translation1.8 Å19.9 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OA5

3oa5


Resolution: 1.8→105.278 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1913 / WRfactor Rwork: 0.1551 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8955 / SU B: 2.176 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1089 / SU Rfree: 0.1088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 10651 5 %RANDOM
Rwork0.1598 ---
all0.1617 212271 --
obs0.1617 212074 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.5 Å2 / Biso mean: 14.8263 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20.06 Å2
2---0.29 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→105.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16574 0 24 1206 17804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02117140
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.97423275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42852189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15824.504786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.499152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1611580
X-RAY DIFFRACTIONr_chiral_restr0.1610.22450
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02113375
X-RAY DIFFRACTIONr_mcbond_it1.2291.510725
X-RAY DIFFRACTIONr_mcangle_it2.056217098
X-RAY DIFFRACTIONr_scbond_it3.32436415
X-RAY DIFFRACTIONr_scangle_it5.0394.56160
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 797 -
Rwork0.212 14886 -
all-15683 -
obs-15683 99.94 %

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