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- PDB-7x78: L-fuculose 1-phosphate aldolase -

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Basic information

Entry
Database: PDB / ID: 7x78
TitleL-fuculose 1-phosphate aldolase
ComponentsL-fuculose phosphate aldolase
KeywordsLYASE / Fuculose 1-phosphate aldolase / Enzyme activity / Klebsiella pneumoniae.
Function / homology
Function and homology information


arabinose catabolic process / L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / L-fucose catabolic process / zinc ion binding
Similarity search - Function
L-fucose phosphate aldolase / 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
Similarity search - Domain/homology
L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLou, X. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural characterization of an L-fuculose-1-phosphate aldolase from Klebsiella pneumoniae.
Authors: Lou, X. / Zhang, J. / Liu, S. / Wang, R. / Li, W. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-fuculose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0805
Polymers23,7671
Non-polymers3124
Water2,864159
1
A: L-fuculose phosphate aldolase
hetero molecules

A: L-fuculose phosphate aldolase
hetero molecules

A: L-fuculose phosphate aldolase
hetero molecules

A: L-fuculose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,31920
Polymers95,0694
Non-polymers1,25016
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 area9350 Å2
ΔGint-242 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.614, 92.614, 41.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein L-fuculose phosphate aldolase / D-ribulose-phosphate aldolase / L-fuculose-1-phosphate aldolase


Mass: 23767.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A6TD81, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.01 M MgCl2, 0.05 M Tris pH 7.5, 1.6 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 15994 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 17.99 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.027 / Net I/σ(I): 25.66
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 5 / Num. unique obs: 787 / CC1/2: 0.945 / Rpim(I) all: 0.142 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FUA

1fua


Resolution: 1.85→25.78 Å / SU ML: 0.1884 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 1596 10 %
Rwork0.1641 14362 -
obs0.1694 15958 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.74 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 16 163 1751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641619
X-RAY DIFFRACTIONf_angle_d0.79062205
X-RAY DIFFRACTIONf_chiral_restr0.0514256
X-RAY DIFFRACTIONf_plane_restr0.0048281
X-RAY DIFFRACTIONf_dihedral_angle_d5.6269217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.27111410.1951273X-RAY DIFFRACTION99.02
1.91-1.980.24261400.18391263X-RAY DIFFRACTION99.72
1.98-2.060.24171430.16741281X-RAY DIFFRACTION100
2.06-2.160.21161430.16871282X-RAY DIFFRACTION99.93
2.16-2.270.24731430.15851288X-RAY DIFFRACTION100
2.27-2.410.23131420.16551287X-RAY DIFFRACTION100
2.41-2.60.19961460.16711307X-RAY DIFFRACTION99.93
2.6-2.860.25331440.16211291X-RAY DIFFRACTION100
2.86-3.270.22521470.15961329X-RAY DIFFRACTION100
3.27-4.120.18591480.14681331X-RAY DIFFRACTION100
4.12-25.780.20251590.16971430X-RAY DIFFRACTION99.75
Refinement TLS params.Method: refined / Origin x: -21.4201583678 Å / Origin y: 51.0788374666 Å / Origin z: 27.6574634293 Å
111213212223313233
T0.129993584546 Å20.0257365921088 Å20.0109615234252 Å2-0.0837253109548 Å20.0218066678845 Å2--0.120026683981 Å2
L2.12669095091 °20.0111847866778 °20.883344772174 °2-0.965791281647 °20.346653575651 °2--2.3022393431 °2
S0.15522118842 Å °0.136431524903 Å °-0.0306157196151 Å °-0.158410534502 Å °-0.095544471726 Å °-0.00254732540088 Å °0.156835606541 Å °-0.0531233671964 Å °-0.0569529164847 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 206)

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