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- PDB-8x2w: Crystal structure of the ancestral GH19 chitinase, Anc4+LoopII (P... -

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Basic information

Entry
Database: PDB / ID: 8x2w
TitleCrystal structure of the ancestral GH19 chitinase, Anc4+LoopII (P12K/N13H/S58T/N193G/Y194F/D197R)
Componentsthe ancestral GH19 chitinase, Anc4+LoopII (P12K/N13H/S58T/N193G/Y194F/D197R)
KeywordsHYDROLASE / GH19 Chitinase
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKozome, D. / Laurino, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Remote loop evolution reveals a complex biological function for chitinase enzymes beyond the active site.
Authors: Kozome, D. / Sljoka, A. / Laurino, P.
History
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: the ancestral GH19 chitinase, Anc4+LoopII (P12K/N13H/S58T/N193G/Y194F/D197R)


Theoretical massNumber of molelcules
Total (without water)25,4441
Polymers25,4441
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.320, 69.590, 70.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein the ancestral GH19 chitinase, Anc4+LoopII (P12K/N13H/S58T/N193G/Y194F/D197R)


Mass: 25444.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.79 Å3/Da / Density % sol: 31.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 uL of Anc4+Loop II+p12K/n13H/s58T/n193G/y194F/d197R (6.0 mg/mL in 10 mM sodium acetate pH 5.0, 150 mM NaCl) + 1 uL of 25% (w/v) polyethylene glycol 3,350, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→49.43 Å / Num. obs: 46885 / % possible obs: 100 % / Redundancy: 52.2 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.992 / Net I/σ(I): 7
Reflection shellResolution: 1.4→1.4 Å / Num. unique obs: 46885 / CC1/2: 0.991 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASER1.20.1_4487phasing
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→49.43 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.1914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2042 2009 5.46 %
Rwork0.1864 34808 -
obs0.1874 36817 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.56 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 0 118 1901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911860
X-RAY DIFFRACTIONf_angle_d1.06082543
X-RAY DIFFRACTIONf_chiral_restr0.0928256
X-RAY DIFFRACTIONf_plane_restr0.0109343
X-RAY DIFFRACTIONf_dihedral_angle_d5.6116256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.27391420.23682469X-RAY DIFFRACTION100
1.44-1.470.23681370.21752423X-RAY DIFFRACTION100
1.47-1.520.22931440.21312449X-RAY DIFFRACTION100
1.52-1.570.221400.18562451X-RAY DIFFRACTION100
1.57-1.620.23951440.18342484X-RAY DIFFRACTION100
1.62-1.690.20471380.1812428X-RAY DIFFRACTION100
1.69-1.760.20981430.18732481X-RAY DIFFRACTION100
1.76-1.860.19381430.18662455X-RAY DIFFRACTION100
1.86-1.970.20271420.18532486X-RAY DIFFRACTION100
1.97-2.130.20411390.1872468X-RAY DIFFRACTION100
2.13-2.340.20711460.18472507X-RAY DIFFRACTION100
2.34-2.680.22471470.19222509X-RAY DIFFRACTION100
2.68-3.370.21811480.1942531X-RAY DIFFRACTION99.96
3.37-49.430.18061560.17642667X-RAY DIFFRACTION99.96

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