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- PDB-6btg: Crystal structure of deoxyribose-phosphate aldolase bound with DH... -

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Basic information

Entry
Database: PDB / ID: 6btg
TitleCrystal structure of deoxyribose-phosphate aldolase bound with DHAP from Bacillus Thuringiensis
ComponentsFuculose phosphate aldolase
KeywordsLYASE / DHAP / 5-deoxyribose / radical SAM enzyme byproduct
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
1,3-DIHYDROXYACETONEPHOSPHATE / : / Fuculose phosphate aldolase
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 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)25,1683
Polymers24,9431
Non-polymers2252
Water4,468248
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)100,67312
Polymers99,7734
Non-polymers9008
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area10200 Å2
ΔGint-77 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.104, 105.104, 49.366
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 200 mM NaCl, 26 % (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: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.698→35.981 Å / Num. obs: 31070 / % possible obs: 99.83 % / Redundancy: 28.2 % / CC1/2: 1 / Rmerge(I) obs: 0.06026 / Rrim(I) all: 0.0614 / Net I/σ(I): 41.77
Reflection shellResolution: 1.698→1.759 Å / Redundancy: 27.9 % / Rmerge(I) obs: 0.5708 / Mean I/σ(I) obs: 6.74 / Num. unique obs: 3017 / CC1/2: 0.96 / Rrim(I) all: 0.0614 / % possible all: 98.43

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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: 1.698→35.981 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1525 4.91 %
Rwork0.1865 --
obs0.1883 31069 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→35.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 11 248 1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071668
X-RAY DIFFRACTIONf_angle_d1.0292254
X-RAY DIFFRACTIONf_dihedral_angle_d13.3628
X-RAY DIFFRACTIONf_chiral_restr0.046248
X-RAY DIFFRACTIONf_plane_restr0.005292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6981-1.75290.28621500.22672577X-RAY DIFFRACTION98
1.7529-1.81550.25731420.22512647X-RAY DIFFRACTION100
1.8155-1.88820.2861200.21372641X-RAY DIFFRACTION100
1.8882-1.97410.25471420.20992656X-RAY DIFFRACTION100
1.9741-2.07820.24241430.20662649X-RAY DIFFRACTION100
2.0782-2.20840.28081400.19922652X-RAY DIFFRACTION100
2.2084-2.37890.23241280.19542697X-RAY DIFFRACTION100
2.3789-2.61820.21491230.19132694X-RAY DIFFRACTION100
2.6182-2.99690.22481490.19472689X-RAY DIFFRACTION100
2.9969-3.77510.21431390.17232750X-RAY DIFFRACTION100
3.7751-35.98870.17841490.15712892X-RAY DIFFRACTION100

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