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- PDB-4xbs: 2-deoxyribose-5-phosphate aldolase mutant - E78K -

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Basic information

Entry
Database: PDB / ID: 4xbs
Title2-deoxyribose-5-phosphate aldolase mutant - E78K
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE / aldolase
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesLactobacillus brevis ATCC 14869 = DSM 20054 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsJiao, X.-C. / Pan, J. / Xu, G.-C. / Kong, X.-D. / Chen, Q. / Zhang, Z.-J. / Xu, J.-H.
CitationJournal: Catalysis Science And Technology / Year: 2015
Title: Efficient synthesis of a statin precursor in high space-time yield by a new aldehyde-tolerant aldolase identified from Lactobacillus brevis
Authors: Jiao, X.-C. / Pan, J. / Xu, G.-C. / Kong, X.-D. / Chen, Q. / Zhang, Z.-J. / Xu, J.-H.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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


Theoretical massNumber of molelcules
Total (without water)56,0992
Polymers56,0992
Non-polymers00
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-21 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.031, 97.031, 118.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein Deoxyribose-phosphate aldolase / 2-deoxyribose-5-phosphate aldolase / DERA / 2-deoxy-D-ribose 5-phosphate aldolase / Phosphodeoxyriboaldolase


Mass: 28049.717 Da / Num. of mol.: 2 / Mutation: E78K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis ATCC 14869 = DSM 20054 (bacteria)
Strain: ATCC 14869 = DSM 20054 / Gene: deoC, HMPREF0495_01319 / Production host: Escherichia coli (E. coli) / References: UniProt: U2PI02, deoxyribose-phosphate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: ammonium acetate, sodium acetate / PH range: 4.3-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 30632 / % possible obs: 100 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.041 / Rrim(I) all: 0.165 / Χ2: 1.011 / Net I/av σ(I): 19.516 / Net I/σ(I): 6.1 / Num. measured all: 477835
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.2515.30.74530150.9230.1960.7711.018100
2.25-2.3415.50.63529790.9320.1660.6571.039100
2.34-2.4415.60.52330080.9540.1360.5411.044100
2.44-2.5715.80.43130160.9650.1120.4451.036100
2.57-2.7315.80.31930240.9820.0820.3291.031100
2.73-2.9515.80.24830450.9890.0640.2571.003100
2.95-3.2415.80.17630550.9940.0450.1821.004100
3.24-3.7115.80.11130690.9970.0290.1150.951100
3.71-4.6715.70.07631180.9990.020.0791.017100
4.67-5014.80.06133030.9990.0160.0630.97199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data processing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
Cootphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→36.572 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 1503 4.92 %
Rwork0.1562 --
obs0.1576 30568 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.07 Å2 / Biso mean: 29.0264 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: final / Resolution: 2.17→36.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 0 328 3540
Biso mean---35.8 -
Num. residues----434

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