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- PDB-6bt9: Chitinase ChiA74 from Bacillus thuringiensis -

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Basic information

Entry
Database: PDB / ID: 6bt9
TitleChitinase ChiA74 from Bacillus thuringiensis
ComponentsChitinase
KeywordsHYDROLASE
Function / homology
Function and homology information


polysaccharide binding / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Cellulose binding domain / 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 ...Cellulose binding domain / 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 / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsJuarez-Hernandez, E. / Brieba, L.G. / Torres-Larios, A. / Jimenez-Sandoval, P. / Barboza-Corona, J.
CitationJournal: Sci Rep / Year: 2019
Title: The crystal structure of the chitinase ChiA74 of Bacillus thuringiensis has a multidomain assembly.
Authors: Juarez-Hernandez, E.O. / Casados-Vazquez, L.E. / Brieba, L.G. / Torres-Larios, A. / Jimenez-Sandoval, P. / Barboza-Corona, J.E.
History
DepositionDec 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)148,6684
Polymers148,5882
Non-polymers802
Water1,40578
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3342
Polymers74,2941
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3342
Polymers74,2941
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.827, 82.407, 101.570
Angle α, β, γ (deg.)90.000, 108.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 40 - 673 / Label seq-ID: 36 - 669

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Chitinase


Mass: 74293.945 Da / Num. of mol.: 2 / Fragment: residues 33-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: BK774_19500 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A243G6Q6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.32 Å3/Da / Density % sol: 46.98 % / Description: Blade-cluster
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) PEG 6000 100 mM HEPES/ Sodium hydroxide pH 7.0 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 25, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.26→62.76 Å / Num. obs: 63274 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.874 / Rmerge(I) obs: 0.301 / Rpim(I) all: 0.143 / Rrim(I) all: 0.335 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1 / Resolution: 2.26→2.31 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.90.48843810.8470.3320.59999.1
5.40.1557060.9650.0730.17299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å62.87 Å
Translation2.4 Å62.87 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.31data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Truncated to A, 1ITX

1itx


Resolution: 2.26→62.76 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.881 / SU B: 10.021 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.231
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 3145 5 %RANDOM
Rwork0.2391 ---
obs0.2398 60010 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.34 Å2 / Biso mean: 22.285 Å2 / Biso min: 3.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å2-0.47 Å2
2--1.3 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 2.26→62.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9341 0 2 78 9421
Biso mean--15.46 11.79 -
Num. residues----1251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0149629
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177948
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.65413190
X-RAY DIFFRACTIONr_angle_other_deg0.9551.64918487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8351255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52524.231442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.196151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1541524
X-RAY DIFFRACTIONr_chiral_restr0.0640.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021939
Refine LS restraints NCS

Ens-ID: 1 / Number: 19033 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.26→2.319 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 218 -
Rwork0.401 4397 -
all-4615 -
obs--99.76 %

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