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- PDB-8x2v: Crystal structure of the ancestral GH19 chitinase, Anc4+LoopII (P... -

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Basic information

Entry
Database: PDB / ID: 8x2v
TitleCrystal structure of the ancestral GH19 chitinase, Anc4+LoopII (P12K/N13H mutant)
ComponentsGH19 chitinase
KeywordsHYDROLASE / GH19 Chitinase
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH19 chitinase


Theoretical massNumber of molelcules
Total (without water)25,4611
Polymers25,4611
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.290, 69.830, 70.270
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 GH19 chitinase


Mass: 25461.275 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.: 134 / 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: 1.8 Å3/Da / Density % sol: 31.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 uL of Anc4+Loop II+p12K/n13H (6.0 mg/mL in 10 mM sodium acetate pH 5.0, 150 mM NaCl) + 1 uL of 25% (w/v) polyethylene glycol 3350, 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: 1.29→49.53 Å / Num. obs: 47133 / % possible obs: 100 % / Redundancy: 33.1 % / Biso Wilson estimate: 12.41 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.87
Reflection shellResolution: 1.29→1.29 Å / Num. unique obs: 47133 / CC1/2: 0.997

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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: 1.29→49.53 Å / SU ML: 0.1172 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.2246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186 2000 4.25 %
Rwork0.1709 45016 -
obs0.1716 47016 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.9 Å2
Refinement stepCycle: LAST / Resolution: 1.29→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 0 134 1928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071881
X-RAY DIFFRACTIONf_angle_d0.95752574
X-RAY DIFFRACTIONf_chiral_restr0.0803257
X-RAY DIFFRACTIONf_plane_restr0.0091349
X-RAY DIFFRACTIONf_dihedral_angle_d5.6941259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.320.24581430.21563185X-RAY DIFFRACTION100
1.32-1.360.24711380.19893136X-RAY DIFFRACTION100
1.36-1.40.21561420.19733196X-RAY DIFFRACTION100
1.4-1.440.21481400.19193162X-RAY DIFFRACTION100
1.44-1.490.2251420.18213198X-RAY DIFFRACTION100
1.49-1.550.20271440.17673183X-RAY DIFFRACTION100
1.55-1.630.20261410.15943185X-RAY DIFFRACTION100
1.63-1.710.19731370.16233174X-RAY DIFFRACTION100
1.71-1.820.19771430.17013184X-RAY DIFFRACTION100
1.82-1.960.21281450.17293225X-RAY DIFFRACTION100
1.96-2.160.18381390.17553218X-RAY DIFFRACTION100
2.16-2.470.16421430.17233248X-RAY DIFFRACTION100
2.47-3.110.20671490.17643293X-RAY DIFFRACTION100
3.11-49.530.14711540.15373429X-RAY DIFFRACTION100

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