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- PDB-3tu9: Crystal structure of rabbit muscle aldolase bound with 5-O-methyl... -

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Basic information

Entry
Database: PDB / ID: 3tu9
TitleCrystal structure of rabbit muscle aldolase bound with 5-O-methyl mannitol 1,6-phosphate
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE/LYASE INHIBITOR / beta-barrel / mammalian aldolase / mannitol-bisphosphate / trypanosomal aldolase / inhibitor docking / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-O-methyl-1,6-di-O-phosphono-D-mannitol / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsArthus-Cartier, G. / Sygusch, J.
CitationJournal: ACS Med Chem Lett / Year: 2011
Title: Mannitol Bis-phosphate Based Inhibitors of Fructose 1,6-Bisphosphate Aldolases.
Authors: Mabiala-Bassiloua, C.G. / Arthus-Cartier, G. / Hannaert, V. / Therisod, H. / Sygusch, J. / Therisod, M.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase A
B: Fructose-bisphosphate aldolase A
C: Fructose-bisphosphate aldolase A
D: Fructose-bisphosphate aldolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,4798
Polymers157,0554
Non-polymers1,4254
Water25,5811420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-42 kcal/mol
Surface area47750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.669, 103.056, 84.458
Angle α, β, γ (deg.)90.00, 98.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fructose-bisphosphate aldolase A / Muscle-type aldolase


Mass: 39263.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: pPB14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-SI / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Sugar
ChemComp-5MM / 2-O-methyl-1,6-di-O-phosphono-D-mannitol


Type: D-saccharide / Mass: 356.158 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H18O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1420 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17.5% PEG4000, 0.1 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2008
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.09→36.973 Å / Num. all: 82812 / Num. obs: 82812 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZAH

1zah


Resolution: 2.09→36.973 Å / SU ML: 0.24 / σ(F): 0.08 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 6199 7.99 %RANDOM
Rwork0.1563 ---
all0.168 82812 --
obs0.1599 77544 93.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.134 Å2 / ksol: 0.43 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8152 Å2-0 Å2-2.5644 Å2
2--5.0074 Å2-0 Å2
3----5.8225 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10682 0 84 1420 12186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710889
X-RAY DIFFRACTIONf_angle_d0.99914756
X-RAY DIFFRACTIONf_dihedral_angle_d14.4764056
X-RAY DIFFRACTIONf_chiral_restr0.0561672
X-RAY DIFFRACTIONf_plane_restr0.0051917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.11350.28291870.22492091X-RAY DIFFRACTION81
2.1135-2.13840.24241820.20342098X-RAY DIFFRACTION85
2.1384-2.16450.26631860.20312193X-RAY DIFFRACTION87
2.1645-2.19180.26021970.19642203X-RAY DIFFRACTION87
2.1918-2.22070.2471960.19792281X-RAY DIFFRACTION89
2.2207-2.25110.24361900.20482154X-RAY DIFFRACTION86
2.2511-2.28330.23961900.19422214X-RAY DIFFRACTION86
2.2833-2.31730.2361920.17272262X-RAY DIFFRACTION90
2.3173-2.35350.221910.16282324X-RAY DIFFRACTION90
2.3535-2.39210.21441960.14962273X-RAY DIFFRACTION90
2.3921-2.43340.18422190.13922321X-RAY DIFFRACTION92
2.4334-2.47760.19651840.14582309X-RAY DIFFRACTION91
2.4776-2.52520.20262120.15112339X-RAY DIFFRACTION93
2.5252-2.57680.21422030.14282408X-RAY DIFFRACTION94
2.5768-2.63280.20812080.14572397X-RAY DIFFRACTION95
2.6328-2.6940.20662030.1442398X-RAY DIFFRACTION95
2.694-2.76140.18772100.1392416X-RAY DIFFRACTION95
2.7614-2.8360.17852190.13532407X-RAY DIFFRACTION95
2.836-2.91940.18462140.13662431X-RAY DIFFRACTION96
2.9194-3.01360.20322200.14142497X-RAY DIFFRACTION98
3.0136-3.12130.20052160.13522486X-RAY DIFFRACTION98
3.1213-3.24620.17582180.13062487X-RAY DIFFRACTION98
3.2462-3.39380.17292120.12792510X-RAY DIFFRACTION99
3.3938-3.57260.15972220.12552512X-RAY DIFFRACTION99
3.5726-3.79620.17122230.11912535X-RAY DIFFRACTION99
3.7962-4.0890.15422170.12282538X-RAY DIFFRACTION100
4.089-4.49980.16592260.12262542X-RAY DIFFRACTION100
4.4998-5.14950.18382230.13972555X-RAY DIFFRACTION99
5.1495-6.48210.22332170.19372559X-RAY DIFFRACTION99
6.4821-36.97860.22972260.23012605X-RAY DIFFRACTION99

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