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- PDB-4xbk: 2-deoxyribose-5-phosphate aldolase from Lactobacillus brevis -

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Basic information

Entry
Database: PDB / ID: 4xbk
Title2-deoxyribose-5-phosphate aldolase from Lactobacillus brevis
ComponentsDeoxyribose-phosphate aldolase
KeywordsLYASE
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
ACETIC ACID / Deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesLactobacillus brevis ATCC 14869 = DSM 20054 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.951 Å
AuthorsJiao, X.-C. / Pan, J. / Xu, G.-C. / Kong, X.-D. / Chen, Q. / Zhang, Z.-J. / Xu, J.-H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyNo. 21276082 China
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2795
Polymers56,0992
Non-polymers1803
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-20 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.882, 96.882, 119.593
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-324-

HOH

21A-379-

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: 28049.650 Da / Num. of mol.: 2
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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
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: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 42101 / % possible obs: 99.9 % / Redundancy: 27.5 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.02 / Rrim(I) all: 0.105 / Χ2: 1.018 / Net I/av σ(I): 28.663 / Net I/σ(I): 15.1 / Num. measured all: 1158340
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0227.20.68441350.9550.1330.6971.01100
2.02-2.127.20.54341240.9650.1060.5531.057100
2.1-2.227.60.35241440.9870.0680.3580.99100
2.2-2.3127.40.30841630.9860.060.3141.092100
2.31-2.4627.90.21941540.9940.0420.2231100
2.46-2.6527.90.17241860.9960.0330.1751100
2.65-2.9128.10.13341900.9970.0250.1351.022100
2.91-3.3328.10.10242360.9980.0190.1040.983100
3.33-4.227.60.07942720.9990.0150.0810.99399.9
4.2-5026.30.05544970.9990.0110.0561.03999.6

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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
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.951→44.898 Å / FOM work R set: 0.8825 / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1784 2120 5.05 %
Rwork0.162 39873 -
obs0.1629 41993 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.55 Å2 / Biso mean: 29.89 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 1.951→44.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 12 430 3654
Biso mean--41.53 38.5 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083284
X-RAY DIFFRACTIONf_angle_d1.0614440
X-RAY DIFFRACTIONf_chiral_restr0.072540
X-RAY DIFFRACTIONf_plane_restr0.004577
X-RAY DIFFRACTIONf_dihedral_angle_d14.2061195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9506-1.99590.23721430.19032575271899
1.9959-2.04580.2331440.18726112755100
2.0458-2.10120.25851470.193526062753100
2.1012-2.1630.21361220.16826392761100
2.163-2.23280.23181300.170326272757100
2.2328-2.31260.20451370.178426372774100
2.3126-2.40520.24111360.1726442780100
2.4052-2.51460.18621320.165926252757100
2.5146-2.64720.18571540.171826482802100
2.6472-2.8130.17891360.163426652801100
2.813-3.03020.20671500.17526512801100
3.0302-3.3350.18161540.168826632817100
3.335-3.81740.1711350.14826882823100
3.8174-4.80860.12531460.13752724287099
4.8086-44.90960.15671540.16272870302499

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