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- PDB-1ktn: Structural Genomics, Protein EC1535 -

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Basic information

Entry
Database: PDB / ID: 1ktn
TitleStructural Genomics, Protein EC1535
Components2-deoxyribose-5-phosphate aldolase
KeywordsSTRUCTURAL GENOMICS / LYASE / BETA BARREL / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / nucleobase-containing small molecule interconversion / carbohydrate catabolic process / lyase activity / DNA damage response / membrane / cytosol
Similarity search - Function
Deoxyribose-phosphate aldolase type II / Deoxyribose-phosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsZhang, R. / Joachimiak, A. / Edwards, A. / Skarina, T. / Evdokimova, E. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.5A crystal structure of 2-deoxyribose-5-phosphate aldlase
Authors: Zhang, R. / Joachimiak, A. / Edwards, A. / Skarina, T. / Evdokimova, E. / Savchenko, A.
History
DepositionJan 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-deoxyribose-5-phosphate aldolase
B: 2-deoxyribose-5-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)53,8302
Polymers53,8302
Non-polymers00
Water11,367631
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.566, 53.558, 81.365
Angle α, β, γ (deg.)90.00, 109.97, 90.00
Int Tables number4
Space group name H-MP1211
DetailsEC1535 existed as monomer. Chain A and Chain B represent two molecules in asymmetric unit.

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Components

#1: Protein 2-deoxyribose-5-phosphate aldolase


Mass: 26914.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Plasmid details: T7 promoter system in BL21(DE3) E. coli strain
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6L0, deoxyribose-phosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 20% PEG4K, 0.2M MgCl2, 0.1M Tris_HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9795, 0.9798, 0.9650
DetectorType: SBC-1 / Detector: CCD / Date: Jan 1, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.9651
ReflectionResolution: 1.4→50 Å / Num. all: 99282 / Num. obs: 98786 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.44 / Num. unique all: 9695 / % possible all: 98.2

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→38.65 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 354397.4 / Data cutoff high rms absF: 354397.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4458 5 %RANDOM
Rwork0.186 ---
obs0.186 88731 88.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6844 Å2 / ksol: 0.373051 e/Å3
Displacement parametersBiso mean: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20.68 Å2
2---0.14 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.4→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 0 631 4393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.199 553 5 %
Rwork0.187 10460 -
obs--66.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMATP.TOP

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