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- PDB-2flf: Crystal structure of l-fuculose-1-phosphate aldolase from Thermus... -

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Basic information

Entry
Database: PDB / ID: 2flf
TitleCrystal structure of l-fuculose-1-phosphate aldolase from Thermus Thermophilus HB8
Componentsfuculose-1-phosphate aldolase
KeywordsLYASE / Class II Aldolase / metal binding / fuculose phosphate / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES
Function / homology
Function and homology information


carbon-carbon lyase 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-1-phosphate aldolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJeyakanthan, J. / Yokoyama, S. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Purification, crystallization and preliminary X-ray crystallographic study of the L-fuculose-1-phosphate aldolase (FucA) from Thermus thermophilus HB8
Authors: Jeyakanthan, J. / Taka, J. / Kikuchi, A. / Kuroishi, C. / Yutani, K. / Shiro, Y.
History
DepositionJan 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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-1-phosphate aldolase
B: fuculose-1-phosphate aldolase
C: fuculose-1-phosphate aldolase
D: fuculose-1-phosphate aldolase
E: fuculose-1-phosphate aldolase
F: fuculose-1-phosphate aldolase
G: fuculose-1-phosphate aldolase
H: fuculose-1-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)172,9668
Polymers172,9668
Non-polymers00
Water4,630257
1
A: fuculose-1-phosphate aldolase
B: fuculose-1-phosphate aldolase
C: fuculose-1-phosphate aldolase
D: fuculose-1-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)86,4834
Polymers86,4834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-44 kcal/mol
Surface area30730 Å2
MethodPISA
2
E: fuculose-1-phosphate aldolase
F: fuculose-1-phosphate aldolase
G: fuculose-1-phosphate aldolase
H: fuculose-1-phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)86,4834
Polymers86,4834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-49 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.405, 101.403, 173.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
fuculose-1-phosphate aldolase / CLASS II ALDOLASE


Mass: 21620.785 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHB9, L-fuculose-phosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 28% PEG 4000, 0.1M CITRATE-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 46644 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.564 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FK5

2fk5


Resolution: 2.7→19.97 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 512801.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 2021 5 %RANDOM
Rwork0.225 ---
obs0.225 40111 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.1263 Å2 / ksol: 0.260732 e/Å3
Displacement parametersBiso mean: 61.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2---11.71 Å20 Å2
3---13.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11637 0 0 257 11894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.521.5
X-RAY DIFFRACTIONc_mcangle_it7.892
X-RAY DIFFRACTIONc_scbond_it7.752
X-RAY DIFFRACTIONc_scangle_it9.812.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 309 4.9 %
Rwork0.308 5950 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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