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- PDB-5jh8: Crystal structure of chitinase from Chromobacterium violaceum ATC... -

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Basic information

Entry
Database: PDB / ID: 5jh8
TitleCrystal structure of chitinase from Chromobacterium violaceum ATCC 12472
ComponentsProbable chitinase
KeywordsHYDROLASE
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 / Glycoside hydrolase superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-6KY / HISTIDINE / Probable chitinase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.018 Å
AuthorsChang, C. / Michalska, K. / Tesar, C. / Clancy, S. / Joachimiak, A.
CitationJournal: To Be Published
Title: Crystal structure of chitinase from Chromobacterium violaceum ATCC 12472
Authors: Chang, C. / Michalska, K. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Structure summary
Revision 1.2Apr 3, 2024Group: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8716
Polymers34,3311
Non-polymers5405
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.030, 67.034, 57.301
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable chitinase


Mass: 34331.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: CV_2736 / Plasmid: pMCSG7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7NUG2

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Non-polymers , 5 types, 572 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-6KY / (2S)-2-(dimethylamino)-4-(methylselanyl)butanoic acid


Type: L-peptide linking / Mass: 224.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO2Se
#5: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.2M Sodium thiocyanate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.5166 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5166 Å / Relative weight: 1
ReflectionResolution: 1.018→40 Å / Num. obs: 156331 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 8.8 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.107 / Net I/av σ(I): 18.256 / Net I/σ(I): 10.8 / Num. measured all: 499029
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.02-1.0430.62378361.05599.9
1.04-1.063.10.51578071.05599.9
1.06-1.083.10.41878811.05599.9
1.08-1.13.10.34777911.10899.8
1.1-1.123.10.27678631.07999.9
1.12-1.153.10.23378391.0899.9
1.15-1.183.10.20578381.09599.9
1.18-1.213.10.18178291.08699.9
1.21-1.243.10.15778571.08899.9
1.24-1.293.10.1478221.0899.8
1.29-1.333.10.11778681.05299.8
1.33-1.383.10.10477751.10399.7
1.38-1.453.20.08778481.08299.6
1.45-1.523.20.0778551.1499.5
1.52-1.623.20.06377801.14299.2
1.62-1.743.20.0677991.1998.9
1.74-1.923.10.05777861.23398.6
1.92-2.23.10.04777471.10698.1
2.2-2.7730.03876801.06197
2.77-404.60.04378301.18997.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2386)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD soluiton from from different wavelength

Resolution: 1.018→16.595 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1479 1568 1 %
Rwork0.1307 --
obs0.1309 156223 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.018→16.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 30 567 3008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072616
X-RAY DIFFRACTIONf_angle_d1.0373572
X-RAY DIFFRACTIONf_dihedral_angle_d12.648917
X-RAY DIFFRACTIONf_chiral_restr0.078369
X-RAY DIFFRACTIONf_plane_restr0.007476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0184-1.05130.2511390.243813464X-RAY DIFFRACTION95
1.0513-1.08880.22231240.199914141X-RAY DIFFRACTION100
1.0888-1.13240.18311590.170314130X-RAY DIFFRACTION100
1.1324-1.18390.15991470.153714126X-RAY DIFFRACTION100
1.1839-1.24630.15081380.142314237X-RAY DIFFRACTION100
1.2463-1.32440.15931280.134814177X-RAY DIFFRACTION100
1.3244-1.42660.13641400.126514127X-RAY DIFFRACTION100
1.4266-1.57010.12811660.113714092X-RAY DIFFRACTION99
1.5701-1.7970.11811360.108414134X-RAY DIFFRACTION99
1.797-2.26320.13891440.11214001X-RAY DIFFRACTION98
2.2632-16.5970.14691470.126814026X-RAY DIFFRACTION98

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