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- PDB-8qps: Deoxyribose-5-phosphate aldolase (DERA) from Geobacillus sp. -

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Basic information

Entry
Database: PDB / ID: 8qps
TitleDeoxyribose-5-phosphate aldolase (DERA) from Geobacillus sp.
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE / Aldolase / Autoinhibition / DERA / Thermophilic
Function / homology
Function and homology information


deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / 2-deoxyribose 1-phosphate catabolic process / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm
Similarity search - Function
Deoxyribose-phosphate aldolase type I / Deoxyribose-phosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesGeobacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsPaakkonen, J. / Hakulinen, N. / Rouvinen, J.
Funding support Finland, 4items
OrganizationGrant numberCountry
Academy of Finland288677 Finland
Academy of Finland287241 Finland
Academy of Finland321514 Finland
Academy of Finland321503 Finland
CitationJournal: To Be Published
Title: Three-dimensional structure of deoxyribose phosphate aldolase (DERA) from thermophilic Geobacillus sp.
Authors: Paakkonen, J. / Andberg, M. / Voutilainen, S. / Koivula, A. / Hakulinen, N. / Janis, J. / Rouvinen, J.
History
DepositionOct 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribose-phosphate aldolase
B: Deoxyribose-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)48,5252
Polymers48,5252
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Dimer dissociation constant ~10 pM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.230, 57.230, 97.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Deoxyribose-phosphate aldolase


Mass: 24262.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. (bacteria) / Gene: deoC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C3D6Y3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 28% PEG 4000, 0.1 M Tris buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 1.64→34.68 Å / Num. obs: 42879 / % possible obs: 98.4 % / Redundancy: 2.56 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.043 / Rrim(I) all: 0.072 / Net I/σ(I): 10.1
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4272 / CC1/2: 0.503 / Rpim(I) all: 0.496 / Rrim(I) all: 0.854 / % possible all: 98.3

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Processing

Software
NameVersionClassification
GDAdata collection
xia20.5.898-g5f4e2fb3-dials-1.14data reduction
DIALS1.14.9-g0c59d74b8-releasedata reduction
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
Aimless0.7.4data scaling
pointless1.11.21data scaling
PHASER2.8.1phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→34.67 Å / SU ML: 0.2453 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.6539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1992 4.65 %Random selection
Rwork0.1916 40884 --
obs0.1937 42876 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.49 Å2
Refinement stepCycle: LAST / Resolution: 1.64→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 280 3496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073337
X-RAY DIFFRACTIONf_angle_d0.86954530
X-RAY DIFFRACTIONf_chiral_restr0.0554547
X-RAY DIFFRACTIONf_plane_restr0.0076588
X-RAY DIFFRACTIONf_dihedral_angle_d20.67931218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.36921480.33732943X-RAY DIFFRACTION98.35
1.68-1.730.32991460.30332898X-RAY DIFFRACTION98.54
1.73-1.780.30611500.2632920X-RAY DIFFRACTION98.87
1.78-1.830.31291380.25332929X-RAY DIFFRACTION98.81
1.83-1.90.29731430.26262954X-RAY DIFFRACTION99.1
1.9-1.980.30881440.22252950X-RAY DIFFRACTION98.82
1.98-2.070.29481410.21032899X-RAY DIFFRACTION98.83
2.07-2.170.28931420.24622952X-RAY DIFFRACTION99.55
2.18-2.310.28361440.23012897X-RAY DIFFRACTION97.78
2.31-2.490.24531300.21572944X-RAY DIFFRACTION98.4
2.49-2.740.24321330.21032919X-RAY DIFFRACTION98.17
2.74-3.140.26211350.20342899X-RAY DIFFRACTION97.65
3.14-3.950.21531500.15992871X-RAY DIFFRACTION97.42
3.95-34.670.17011480.13882909X-RAY DIFFRACTION98.01

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