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- PDB-5zol: Crystal structure of a three sites mutantion of FSAA complexed wi... -

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Basic information

Entry
Database: PDB / ID: 5zol
TitleCrystal structure of a three sites mutantion of FSAA complexed with HA and product
ComponentsFructose-6-phosphate aldolase 1
KeywordsLYASE / Fructose-6-phosphate aldolase / donor / acceptor / mutant / flexible
Function / homology
Function and homology information


fructose 6-phosphate aldolase activity / ketone catabolic process / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel ...Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-hydroxypropan-2-one / thiophene-2-carbaldehyde / Chem-LW2 / Fructose-6-phosphate aldolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.172 Å
AuthorsWu, L. / Yang, X.H. / Yu, H.W. / Zhou, J.H.
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: The engineering of decameric d-fructose-6-phosphate aldolase A by combinatorial modulation of inter- and intra-subunit interactions.
Authors: Yang, X. / Wu, L. / Li, A. / Ye, L. / Zhou, J. / Yu, H.
History
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-6-phosphate aldolase 1
B: Fructose-6-phosphate aldolase 1
C: Fructose-6-phosphate aldolase 1
D: Fructose-6-phosphate aldolase 1
E: Fructose-6-phosphate aldolase 1
F: Fructose-6-phosphate aldolase 1
G: Fructose-6-phosphate aldolase 1
H: Fructose-6-phosphate aldolase 1
I: Fructose-6-phosphate aldolase 1
J: Fructose-6-phosphate aldolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,81643
Polymers269,28010
Non-polymers3,53533
Water16,448913
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39690 Å2
ΔGint-453 kcal/mol
Surface area72450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.085, 103.085, 492.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11G-465-

HOH

21G-519-

HOH

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Fructose-6-phosphate aldolase 1 / Fructose-6-phosphate aldolase A / FSAA


Mass: 26928.037 Da / Num. of mol.: 10 / Mutation: T31I/T59Q/Q195I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fsaA, fsa, mipB, ybiZ, b0825, JW5109 / Production host: Escherichia coli (E. coli)
References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases

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Non-polymers , 6 types, 946 molecules

#2: Chemical
ChemComp-4Y8 / 1-hydroxypropan-2-one / Hydroxyacetone


Mass: 74.079 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C3H6O2
#3: Chemical
ChemComp-LW2 / (3S,4S)-3,4-dihydroxy-4-(thiophen-2-yl)butan-2-one


Mass: 186.228 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H10O3S
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-LW1 / thiophene-2-carbaldehyde / Thiophene-2-carboxaldehyde


Mass: 112.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4OS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Hepes pH7.2, 18% PEG 4000, 10% isopropyl alcohol, 0.2M ammonium sulfate, 0.01M disodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 161347 / % possible obs: 99.7 % / Redundancy: 16.3 % / Net I/σ(I): 2
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 15.8 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 2.172→22.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.43
RfactorNum. reflection% reflection
Rfree0.232 7801 4.99 %
Rwork0.1908 --
obs0.1929 156443 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.172→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16191 0 204 913 17308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816683
X-RAY DIFFRACTIONf_angle_d0.90422684
X-RAY DIFFRACTIONf_dihedral_angle_d4.44712221
X-RAY DIFFRACTIONf_chiral_restr0.0522768
X-RAY DIFFRACTIONf_plane_restr0.0052905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1723-2.1970.34362030.27823258X-RAY DIFFRACTION64
2.197-2.22280.33881840.26733843X-RAY DIFFRACTION77
2.2228-2.24990.33042520.27774406X-RAY DIFFRACTION87
2.2499-2.27830.34672460.26264719X-RAY DIFFRACTION94
2.2783-2.30830.28572250.25554930X-RAY DIFFRACTION97
2.3083-2.33990.30412460.25255042X-RAY DIFFRACTION98
2.3399-2.37330.29292660.25534918X-RAY DIFFRACTION99
2.3733-2.40860.31252820.245032X-RAY DIFFRACTION99
2.4086-2.44620.32630.24085049X-RAY DIFFRACTION100
2.4462-2.48630.27442610.23385046X-RAY DIFFRACTION100
2.4863-2.52910.32082430.23775111X-RAY DIFFRACTION100
2.5291-2.5750.29122420.23485108X-RAY DIFFRACTION100
2.575-2.62450.30223320.22454988X-RAY DIFFRACTION100
2.6245-2.6780.26183040.22124996X-RAY DIFFRACTION100
2.678-2.73610.27982290.21755126X-RAY DIFFRACTION100
2.7361-2.79970.25432410.22115121X-RAY DIFFRACTION100
2.7997-2.86950.29622610.22375082X-RAY DIFFRACTION100
2.8695-2.9470.27262430.22435114X-RAY DIFFRACTION100
2.947-3.03350.26542830.21145087X-RAY DIFFRACTION100
3.0335-3.13120.26132430.21625119X-RAY DIFFRACTION100
3.1312-3.24280.27052630.21155069X-RAY DIFFRACTION100
3.2428-3.37220.25582560.20155125X-RAY DIFFRACTION100
3.3722-3.52520.21822870.17835104X-RAY DIFFRACTION100
3.5252-3.71030.20022600.17775161X-RAY DIFFRACTION100
3.7103-3.94160.19993010.15585124X-RAY DIFFRACTION100
3.9416-4.24410.16762570.15075169X-RAY DIFFRACTION100
4.2441-4.66780.16022810.13495158X-RAY DIFFRACTION100
4.6678-5.33560.18572820.13645144X-RAY DIFFRACTION99
5.3356-6.69360.19772940.16275158X-RAY DIFFRACTION98
6.6936-22.7010.14482710.13445335X-RAY DIFFRACTION96

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