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- PDB-4w5u: Crystal structure of chitinase 40 from thermophilic bacteria Stre... -

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Basic information

Entry
Database: PDB / ID: 4w5u
TitleCrystal structure of chitinase 40 from thermophilic bacteria Streptomyces thermoviolaceus.
ComponentsChitinase
KeywordsHYDROLASE / TIM barrel / temperature adaptation
Function / homology
Function and homology information


chitin binding / carbohydrate metabolic process
Similarity search - Function
Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases ...Chitinase A; domain 3 - #10 / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Chitinase
Similarity search - Component
Biological speciesStreptomyces thermoviolaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.771 Å
AuthorsMalecki, P.H. / Vorgias, C.E. / Rypniewski, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
The project was co-funded by the European Union within the European Regional Development Fund Poland
CitationJournal: Int J Mol Sci / Year: 2020
Title: The Crystal Structure of a Streptomyces thermoviolaceus Thermophilic Chitinase Known for Its Refolding Efficiency
Authors: Malecki, P.H. / Bejger, M. / Rypniewski, W. / Vorgias, C.E.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Apr 29, 2020Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.1May 1, 2024Group: 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
B: Chitinase
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8734
Polymers86,6692
Non-polymers2042
Water1,33374
1
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4372
Polymers43,3351
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4372
Polymers43,3351
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.150, 183.150, 130.814
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-604-

HOH

21B-616-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYchain AAB40 - 40840 - 408
2ASNASNchain BBA39 - 40839 - 408

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Components

#1: Protein Chitinase


Mass: 43334.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Secretion signal peptide has been recognized and processed by E. coli.
Source: (gene. exp.) Streptomyces thermoviolaceus (bacteria)
Gene: chi40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56077, chitinase
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.9 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2012
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 332669 / Rmerge(I) obs: 0.149 / Χ2: 1.08 / D res high: 2.77 Å / Num. obs: 33170 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
8.2149143310.041
5.848.21236610.059
4.785.84297110.076
4.154.78347110.094
3.714.15387910.138
3.393.71427610.217
3.143.39464010.372
2.943.14496410.65
2.772.94517011.008
ReflectionResolution: 2.77→49 Å / Num. all: 33170 / Num. obs: 33170 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 10.03 % / Biso Wilson estimate: 57.58 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.157 / Χ2: 1.076 / Net I/σ(I): 13.53 / Num. measured all: 332669
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.77-2.949.790.8741.0081.9150596527251701.06398.1
2.94-3.140.9530.653.352359496549640.683100
3.14-3.390.9830.3725.9548725465146400.39199.8
3.39-3.710.9930.21710.4944318429342760.22999.6
3.71-4.150.9950.13816.8939159390638790.14599.3
4.15-4.780.9970.09423.133943348334710.09999.7
4.78-5.840.9980.07626.3128894297229710.08100
5.84-8.210.9990.05930.8922448236723660.062100
8.210.9990.04137.0312227144814330.04399

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.37 Å49.02 Å
Translation6.37 Å49.02 Å

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Processing

Software
NameVersionClassification
XDS2.5.1data reduction
PHENIXmodel building
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1772)refinement
Aimlessdata scaling
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The model structure was generated by the GeneSilico Metaserver.

Resolution: 2.771→49 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 995 3 %Random selection
Rwork0.1498 32149 --
obs0.1515 33144 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.29 Å2 / Biso mean: 64.2189 Å2 / Biso min: 24.84 Å2
Refinement stepCycle: final / Resolution: 2.771→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 14 74 5660
Biso mean--98.86 55.56 -
Num. residues----739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145756
X-RAY DIFFRACTIONf_angle_d1.4787851
X-RAY DIFFRACTIONf_chiral_restr0.065809
X-RAY DIFFRACTIONf_plane_restr0.0081038
X-RAY DIFFRACTIONf_dihedral_angle_d14.1111921
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3252X-RAY DIFFRACTION8.787TORSIONAL
12B3252X-RAY DIFFRACTION8.787TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7706-2.91660.3241370.25944419455698
2.9166-3.09930.26341410.221545434684100
3.0993-3.33860.26341400.198445274667100
3.3386-3.67440.24071410.15954557469899
3.6744-4.20590.1981420.13054571471399
4.2059-5.2980.1661430.110946384781100
5.298-49.02620.17881510.13448945045100

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