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- PDB-6z9h: Escherichia coli D-2-deoxyribose-5-phosphate aldolase - C47V/G204... -

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Basic information

Entry
Database: PDB / ID: 6z9h
TitleEscherichia coli D-2-deoxyribose-5-phosphate aldolase - C47V/G204A/S239D 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 / cytoplasm / 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-type TIM barrel
Similarity search - Domain/homology
FORMIC ACID / Deoxyribose-phosphate aldolase / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,6086
Polymers57,4142
Non-polymers1944
Water10,377576
1
A: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8153
Polymers28,7071
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7933
Polymers28,7071
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.750, 53.870, 80.530
Angle α, β, γ (deg.)90.000, 110.680, 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: 28706.801 Da / Num. of mol.: 2 / Mutation: C47V/G204A/S239D
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, magnesium formate, BIS-TRIS

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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: 1.58→39.41 Å / Num. obs: 51138 / % possible obs: 96.9 % / Redundancy: 1.76 % / Biso Wilson estimate: 20.14 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.123 / Net I/σ(I): 8.5
Reflection shellResolution: 1.72→1.78 Å / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5131 / CC1/2: 0.503 / Rrim(I) all: 0.653

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Processing

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

1ktn


Resolution: 1.72→38.35 Å / SU ML: 0.2543 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4964 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 2476 4.84 %Random selection
Rwork0.1818 48654 --
obs0.184 51130 96.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.58 Å2
Refinement stepCycle: LAST / Resolution: 1.72→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 8 576 4329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853836
X-RAY DIFFRACTIONf_angle_d0.94365199
X-RAY DIFFRACTIONf_chiral_restr0.057620
X-RAY DIFFRACTIONf_plane_restr0.0064677
X-RAY DIFFRACTIONf_dihedral_angle_d12.88062362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.750.38161420.29642713X-RAY DIFFRACTION97.91
1.75-1.790.28671360.26212709X-RAY DIFFRACTION97.5
1.79-1.830.29491350.24262684X-RAY DIFFRACTION96.91
1.83-1.870.27751330.2282705X-RAY DIFFRACTION97.06
1.87-1.920.28151480.21832654X-RAY DIFFRACTION96.49
1.92-1.970.26261240.21532662X-RAY DIFFRACTION96.14
1.97-2.030.27131470.22082653X-RAY DIFFRACTION96.25
2.03-2.090.28741320.22042659X-RAY DIFFRACTION95.32
2.09-2.170.28241370.232685X-RAY DIFFRACTION96.45
2.17-2.250.2791510.21592672X-RAY DIFFRACTION96.25
2.25-2.360.28341300.21192708X-RAY DIFFRACTION97.06
2.36-2.480.28021460.2242677X-RAY DIFFRACTION96.02
2.48-2.640.28611330.21752664X-RAY DIFFRACTION96.38
2.64-2.840.22211070.19242728X-RAY DIFFRACTION95.71
2.84-3.120.23791460.18152711X-RAY DIFFRACTION97.31
3.12-3.580.19181430.14812745X-RAY DIFFRACTION97.93
3.58-4.510.14421420.11762789X-RAY DIFFRACTION98.59
4.51-38.350.14031440.12482836X-RAY DIFFRACTION97.96

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