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- PDB-6z9j: Escherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K mutant -

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Basic information

Entry
Database: PDB / ID: 6z9j
TitleEscherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K mutant
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE / Aldolase / DERA
Function / homology
Function and homology information


deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / 2-deoxyribose 1-phosphate catabolic process / deoxyribonucleotide catabolic process / nucleobase-containing small molecule interconversion / carbohydrate catabolic process / lyase activity / DNA damage response / membrane / cytosol / cytoplasm
Similarity search - Function
Deoxyribose-phosphate aldolase type II / 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 / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPaakkonen, J. / Hakulinen, N. / Rouvinen, J.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland288677 Finland
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2020
Title: Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods.
Authors: Voutilainen, S. / Heinonen, M. / Andberg, M. / Jokinen, E. / Maaheimo, H. / Paakkonen, J. / Hakulinen, N. / Rouvinen, J. / Lahdesmaki, H. / Kaski, S. / Rousu, J. / Penttila, M. / Koivula, A.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Deoxyribose-phosphate aldolase
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,07911
Polymers53,8602
Non-polymers2199
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Experimental dissociation constant ~ 2 * 10^-6 mol/l
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-55 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.504, 52.811, 80.675
Angle α, β, γ (deg.)90.000, 111.230, 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 Deoxyribose-phosphate aldolase / DERA / 2-deoxy-D-ribose 5-phosphate aldolase / Phosphodeoxyriboaldolase / Deoxyriboaldolase


Mass: 26930.033 Da / Num. of mol.: 2 / Mutation: N21K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: deoC, A6592_04055, A9819_24930, AJ318_04090, AML35_20375, AWE53_009755, AWF59_004780, AWG90_001355, AZZ83_003140, B9M99_13055, BHF46_08905, BIU72_19175, BIZ41_21315, BK292_12675, BK296_03525, ...Gene: deoC, A6592_04055, A9819_24930, AJ318_04090, AML35_20375, AWE53_009755, AWF59_004780, AWG90_001355, AZZ83_003140, B9M99_13055, BHF46_08905, BIU72_19175, BIZ41_21315, BK292_12675, BK296_03525, BK375_05655, BON91_08010, BvCmsC61A_04176, BvCmsHHP001_01002, BvCmsKKP061_00143, BvCmsKSP045_01273, BvCmsKSP067_04018, BvCmsKSP076_01350, BvCmsNSP047_00091, BvCmsSINP022_00140, BZL69_04490, C4M78_04295, C7B08_10715, C7B18_26170, CDC27_23655, D2188_24830, D3P01_08005, D9D31_02570, D9E34_05115, D9G48_24275, D9I87_14825, D9I88_23755, D9K54_15785, DD762_00045, DND16_14490, DNQ45_13620, DTL90_19480, DTM45_25725, DU321_02660, DXT71_19415, E0L12_12025, E5S46_05005, E5S58_22595, E5S61_04910, EC382_07685, EL79_3891, EL80_3836, ELT23_13160, ELV08_18870, ELV15_04550, ELV28_15080, EQ825_04285, EQ830_02895, ERS085386_00787, EVY14_13465, EXX13_04350, EXX23_12990, EXX53_09895, EYY34_19360, FNJ83_01355, FV438_05665, FWK02_17600, FY127_22350, HMPREF3040_02396, NCTC10090_02419, NCTC7922_05561, NCTC9117_05294, NCTC9777_00681, NCTC9969_04462, PGD_03624, SAMEA3472056_01168, SAMEA3472108_04807, SAMEA3485101_00909, SAMEA3485113_03629, SAMEA3752559_04076, SAMEA3753300_03100, UC41_15640
Plasmid: pBAT4 / Production host: Escherichia coli (E. coli)
References: UniProt: E2QLE1, UniProt: P0A6L0*PLUS, deoxyribose-phosphate aldolase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 4000, magnesium formate, TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.5→31.31 Å / Num. obs: 74834 / % possible obs: 98.3 % / Redundancy: 1.82 % / Biso Wilson estimate: 17.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7258 / CC1/2: 0.637 / Rrim(I) all: 0.764 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MxCuBEdata collection
PHASERphasing
Coot0.8.9model building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KTN

1ktn


Resolution: 1.5→31.3 Å / SU ML: 0.1723 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1319 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 3768 5.04 %Random selection
Rwork0.1594 71050 --
obs0.1608 74818 98.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.32 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 9 569 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673929
X-RAY DIFFRACTIONf_angle_d0.93115330
X-RAY DIFFRACTIONf_chiral_restr0.0567629
X-RAY DIFFRACTIONf_plane_restr0.0065693
X-RAY DIFFRACTIONf_dihedral_angle_d11.40322432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.35351700.33482498X-RAY DIFFRACTION94.58
1.52-1.540.35581410.31552537X-RAY DIFFRACTION96.71
1.54-1.560.3211300.28962627X-RAY DIFFRACTION97.42
1.56-1.580.28621530.27082608X-RAY DIFFRACTION98.5
1.58-1.610.31561540.25962614X-RAY DIFFRACTION98.75
1.61-1.630.25511150.23982645X-RAY DIFFRACTION98.75
1.63-1.660.24431350.22792594X-RAY DIFFRACTION98.98
1.66-1.690.26861330.21132687X-RAY DIFFRACTION99.02
1.69-1.720.23081320.20992650X-RAY DIFFRACTION98.93
1.72-1.750.22361530.1982638X-RAY DIFFRACTION99.22
1.75-1.790.21721260.18212648X-RAY DIFFRACTION99.04
1.79-1.820.21241630.17432640X-RAY DIFFRACTION99.43
1.82-1.870.25211350.1672628X-RAY DIFFRACTION99.17
1.87-1.910.20611320.16862672X-RAY DIFFRACTION99.15
1.91-1.970.18831250.16492664X-RAY DIFFRACTION99.01
1.97-2.020.18371310.16252670X-RAY DIFFRACTION99.54
2.02-2.090.16041210.14612639X-RAY DIFFRACTION98.64
2.09-2.160.19661450.14252625X-RAY DIFFRACTION98.23
2.16-2.250.16141540.13642643X-RAY DIFFRACTION98.62
2.25-2.350.1861430.14422607X-RAY DIFFRACTION98.39
2.35-2.480.17071560.15262604X-RAY DIFFRACTION98.15
2.48-2.630.18831260.15582660X-RAY DIFFRACTION97.55
2.63-2.830.15771410.15262619X-RAY DIFFRACTION97.98
2.83-3.120.17981280.15182670X-RAY DIFFRACTION98.14
3.12-3.570.18641120.14122665X-RAY DIFFRACTION97.92
3.57-4.50.14451530.1182616X-RAY DIFFRACTION96.78
4.5-31.30.15591610.14542682X-RAY DIFFRACTION96.67

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