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- PDB-8hne: Crystal structure of the ancestral GH19 chitinase Anc4 -

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Basic information

Entry
Database: PDB / ID: 8hne
TitleCrystal structure of the ancestral GH19 chitinase Anc4
ComponentsAnc4, ancestral GH19 chitinase
KeywordsHYDROLASE / GH19 Chitinase
Function / homologyChem-1PG
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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
DepositionDec 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anc4, ancestral GH19 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6914
Polymers24,0491
Non-polymers6433
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.140, 76.240, 78.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Anc4, ancestral GH19 chitinase


Mass: 24048.719 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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 316 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) polyethylene glycol monomethyl ether 2000, 0.1M MES monohydrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→39.47 Å / Num. obs: 73261 / % possible obs: 99.62 % / Redundancy: 2 % / Biso Wilson estimate: 8.18 Å2 / CC1/2: 0.899 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.172 / Rrim(I) all: 0.2433 / Net I/σ(I): 4.14
Reflection shellResolution: 1.13→1.17 Å / Rmerge(I) obs: 0.2298 / Num. unique obs: 6976

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→39.47 Å / SU ML: 0.1175 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.0227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2505 2002 2.73 %
Rwork0.2407 71259 -
obs0.241 73261 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.88 Å2
Refinement stepCycle: LAST / Resolution: 1.13→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 41 214 1947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741793
X-RAY DIFFRACTIONf_angle_d1.09092441
X-RAY DIFFRACTIONf_chiral_restr0.0749245
X-RAY DIFFRACTIONf_plane_restr0.0088324
X-RAY DIFFRACTIONf_dihedral_angle_d11.6078270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.26591290.24664804X-RAY DIFFRACTION95.08
1.16-1.190.23941430.22215045X-RAY DIFFRACTION99.81
1.19-1.220.21691440.2125011X-RAY DIFFRACTION99.96
1.22-1.260.2371430.21275042X-RAY DIFFRACTION99.98
1.26-1.310.21621400.215055X-RAY DIFFRACTION99.98
1.31-1.360.23281400.21325068X-RAY DIFFRACTION100
1.36-1.420.24821410.21845058X-RAY DIFFRACTION100
1.42-1.50.23041500.22625075X-RAY DIFFRACTION100
1.5-1.590.25131410.23585096X-RAY DIFFRACTION100
1.59-1.720.26531460.24765108X-RAY DIFFRACTION99.96
1.72-1.890.261430.26785148X-RAY DIFFRACTION100
1.89-2.160.2741430.26915126X-RAY DIFFRACTION100
2.16-2.720.29531490.25765196X-RAY DIFFRACTION100
2.72-39.470.2251500.23575427X-RAY DIFFRACTION99.93

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