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- PDB-6btd: Crystal structure of deoxyribose-phosphate aldolase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 6btd
TitleCrystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose
ComponentsFuculose phosphate aldolase
KeywordsLYASE / 5-deoxyribose / radical SAM enzyme byproduct / aldolase
Function / homology
Function and homology information


L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity
Similarity search - Function
L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Fuculose phosphate aldolase
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsLi, Q. / Bruner, S.D.
CitationJournal: Nat Commun / Year: 2018
Title: Salvage of the 5-deoxyribose byproduct of radical SAM enzymes.
Authors: Beaudoin, G.A.W. / Li, Q. / Folz, J. / Fiehn, O. / Goodsell, J.L. / Angerhofer, A. / Bruner, S.D. / Hanson, A.D.
History
DepositionDec 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Fuculose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0943
Polymers24,9431
Non-polymers1512
Water3,675204
1
A: Fuculose phosphate aldolase
hetero molecules

A: Fuculose phosphate aldolase
hetero molecules

A: Fuculose phosphate aldolase
hetero molecules

A: Fuculose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,37712
Polymers99,7734
Non-polymers6048
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area8760 Å2
ΔGint-124 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.724, 103.724, 48.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Fuculose phosphate aldolase


Mass: 24943.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: BK775_23715, CCZ40_07290 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: A0A231I520, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 200 mM NaCl, 25 % (v/v) PEG-3350, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.55→35.55 Å / Num. obs: 39118 / % possible obs: 99.93 % / Redundancy: 28.7 % / CC1/2: 1 / Rmerge(I) obs: 0.06302 / Rrim(I) all: 0.06417 / Net I/σ(I): 41.73
Reflection shellResolution: 1.551→1.606 Å / Redundancy: 28.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 7.37 / Num. unique obs: 3800 / CC1/2: 0.973 / Rrim(I) all: 0.06417 / % possible all: 99.29

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C24

4c24


Resolution: 1.551→35.547 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 1941 4.96 %
Rwork0.1646 --
obs0.1655 39117 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.551→35.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 6 204 1794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061626
X-RAY DIFFRACTIONf_angle_d12199
X-RAY DIFFRACTIONf_dihedral_angle_d12.292609
X-RAY DIFFRACTIONf_chiral_restr0.042245
X-RAY DIFFRACTIONf_plane_restr0.005284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5511-1.58990.22731110.18452613X-RAY DIFFRACTION99
1.5899-1.63290.19221310.17222625X-RAY DIFFRACTION100
1.6329-1.68090.17941270.16852621X-RAY DIFFRACTION100
1.6809-1.73520.20851420.16832615X-RAY DIFFRACTION100
1.7352-1.79720.18241350.16552605X-RAY DIFFRACTION100
1.7972-1.86910.16371530.16162607X-RAY DIFFRACTION100
1.8691-1.95420.20131420.15682646X-RAY DIFFRACTION100
1.9542-2.05720.17891660.15652571X-RAY DIFFRACTION100
2.0572-2.18610.17451180.15622669X-RAY DIFFRACTION100
2.1861-2.35490.19241280.16032674X-RAY DIFFRACTION100
2.3549-2.59180.16081230.15972694X-RAY DIFFRACTION100
2.5918-2.96670.18661290.16872685X-RAY DIFFRACTION100
2.9667-3.7370.16651520.16072715X-RAY DIFFRACTION100
3.737-35.55590.18511840.17272836X-RAY DIFFRACTION100

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