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- PDB-8hnf: Crystal structure of the ancestral GH19 chitinase Anc5 -

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Basic information

Entry
Database: PDB / ID: 8hnf
TitleCrystal structure of the ancestral GH19 chitinase Anc5
ComponentsAnc5, ancestral GH19 chitinase
KeywordsHYDROLASE / GH19 Chitinase
Function / homologyChem-1PG
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anc5, ancestral GH19 chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7043
Polymers26,2561
Non-polymers4482
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.888, 73.427, 39.279
Angle α, β, γ (deg.)90.000, 99.970, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Anc5, ancestral GH19 chitinase


Mass: 26256.355 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.: 1 / 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.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 316 K / Method: vapor diffusion, hanging drop
Details: 27% (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: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→38.69 Å / Num. obs: 28613 / % possible obs: 99.54 % / Redundancy: 2 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.06581 / Net I/σ(I): 10.36
Reflection shellResolution: 1.57→1.627 Å / Rmerge(I) obs: 0.4842 / Num. unique obs: 2773

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→38.69 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.8092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2004 1435 5.02 %
Rwork0.176 27172 -
obs0.1772 28607 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.28 Å2
Refinement stepCycle: LAST / Resolution: 1.57→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 29 86 1960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01021967
X-RAY DIFFRACTIONf_angle_d1.09162678
X-RAY DIFFRACTIONf_chiral_restr0.0564264
X-RAY DIFFRACTIONf_plane_restr0.0121354
X-RAY DIFFRACTIONf_dihedral_angle_d12.8604287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.630.35651300.32482641X-RAY DIFFRACTION96.92
1.63-1.690.33161440.2682706X-RAY DIFFRACTION100
1.69-1.770.29321660.22222706X-RAY DIFFRACTION99.97
1.77-1.860.25751440.19452709X-RAY DIFFRACTION99.89
1.86-1.980.23541770.19642683X-RAY DIFFRACTION99.97
1.98-2.130.22381300.16952737X-RAY DIFFRACTION99.83
2.13-2.350.20051190.16762748X-RAY DIFFRACTION99.65
2.35-2.690.18881470.16282722X-RAY DIFFRACTION99.86
2.69-3.380.18921320.17112754X-RAY DIFFRACTION99.97
3.38-38.690.1581460.1572766X-RAY DIFFRACTION99.35

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