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- PDB-8di1: Bfo2294: Tannerella forsythia 2-Keto-3-deoxy-6-phosphogluconate a... -

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Basic information

Entry
Database: PDB / ID: 8di1
TitleBfo2294: Tannerella forsythia 2-Keto-3-deoxy-6-phosphogluconate aldolase (KDPG) and 4-Hydroxy-2-oxoglutarate aldolase (KHG)
ComponentsKDPG and KHG aldolase
KeywordsLYASE
Function / homologyKDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase-type TIM barrel / lyase activity / KDPG and KHG aldolase
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSuits, M.D.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)DDG-2020-00007 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-05018 Canada
CitationJournal: Plos One / Year: 2022
Title: Degradation of chondroitin sulfate A by a PUL-like operon in Tannerella forsythia.
Authors: Nguyen, P. / Eshaque, R. / Garland, B.A. / Dang, A. / Suits, M.D.L.
History
DepositionJun 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: 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 / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KDPG and KHG aldolase


Theoretical massNumber of molelcules
Total (without water)24,3031
Polymers24,3031
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.150, 98.150, 98.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-326-

HOH

31A-334-

HOH

41A-383-

HOH

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Components

#1: Protein KDPG and KHG aldolase


Mass: 24303.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (strain ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338) (bacteria)
Strain: ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338
Gene: BFO_2294 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G8UJX2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% (v/v) Tacsimate pH 7.0 and 11% (v/v) Tacsimate pH 9.0 and 6.5% (v/v) glycerol as the crystallization solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97948 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.2→43.89 Å / Num. obs: 16309 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 33.97 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.041 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2348 / CC1/2: 0.878 / Rpim(I) all: 0.216 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WA3

1wa3


Resolution: 2.2→34.7 Å / SU ML: 0.2203 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.2176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 784 4.81 %
Rwork0.1792 15523 -
obs0.1812 16307 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 0 89 1736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281694
X-RAY DIFFRACTIONf_angle_d0.60572305
X-RAY DIFFRACTIONf_chiral_restr0.0445260
X-RAY DIFFRACTIONf_plane_restr0.0039300
X-RAY DIFFRACTIONf_dihedral_angle_d4.207236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.26071190.20292579X-RAY DIFFRACTION99.93
2.34-2.520.24361400.18412522X-RAY DIFFRACTION100
2.52-2.770.25731380.22162551X-RAY DIFFRACTION100
2.77-3.170.22661220.19282579X-RAY DIFFRACTION99.96
3.17-3.990.21661280.16932592X-RAY DIFFRACTION100
4-34.70.19781370.16322700X-RAY DIFFRACTION100

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