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- PDB-8tnf: Crystal structure of sulfohexulose-1-phosphate aldolase from Para... -

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Basic information

Entry
Database: PDB / ID: 8tnf
TitleCrystal structure of sulfohexulose-1-phosphate aldolase from Paracoccus onubensis strain Merri
ComponentsDUF2090 domain-containing protein
KeywordsLYASE / sulfohexulose-1-phosphate aldolase
Function / homology: / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase-type TIM barrel / lyase activity / DUF2090 domain-containing protein
Function and homology information
Biological speciesParacoccus onubensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210100233, DP210100233 Australia
CitationJournal: To Be Published
Title: A patchwork pathway for catabolism degradation of the sulfosugar sulfofucose
Authors: Li, J. / Lee, M. / Yang, S. / Lewis, J.M. / Herisse, M. / Pidot, S.J. / Scott, N.E. / Williams, S.J.
History
DepositionAug 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF2090 domain-containing protein
B: DUF2090 domain-containing protein
C: DUF2090 domain-containing protein
D: DUF2090 domain-containing protein
E: DUF2090 domain-containing protein
F: DUF2090 domain-containing protein
G: DUF2090 domain-containing protein
H: DUF2090 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)321,2118
Polymers321,2118
Non-polymers00
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.663, 82.485, 144.77
Angle α, β, γ (deg.)96.05, 90, 97.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DUF2090 domain-containing protein


Mass: 40151.359 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus onubensis (bacteria) / Strain: Merrie / Gene: D3P04_00185 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A418T8G4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 0.2 M L-proline, 14-18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→47.98 Å / Num. obs: 121327 / % possible obs: 97.7 % / Redundancy: 1.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.077 / Net I/σ(I): 4.9
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 5943 / CC1/2: 0.538

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.88 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.879 / SU R Cruickshank DPI: 0.45 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.412 / SU Rfree Blow DPI: 0.284 / SU Rfree Cruickshank DPI: 0.295
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 6050 -RANDOM
Rwork0.2368 ---
obs0.239 121306 97.7 %-
Displacement parametersBiso mean: 52.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.125 Å21.5217 Å22.6093 Å2
2--7.3371 Å22.4939 Å2
3----6.2121 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20600 0 0 484 21084
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00721047HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.928564HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7247SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3620HARMONIC5
X-RAY DIFFRACTIONt_it21047HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2665SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact18414SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion17.31
LS refinement shellResolution: 2.5→2.52 Å
RfactorNum. reflection% reflection
Rfree0.3539 123 -
Rwork0.3254 --
obs0.3269 2427 95.91 %

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