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- PDB-5f4x: Fructose-1,6-bisphosphate aldolase K229M mutant from rabbit muscle -

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Basic information

Entry
Database: PDB / ID: 5f4x
TitleFructose-1,6-bisphosphate aldolase K229M mutant from rabbit muscle
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / Aldolase / Class I / Lysine mutant
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 / glycolytic process / protein homotetramerization / positive regulation of cell migration
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
Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLowKam, C. / Arthus-Cartier, G.
CitationJournal: To Be Published
Title: DECYCLIZATION DETERMINES DIASTEREOISOMERIC SUBSTRATE SPECIFICITY OF MAMMALIAN CLASS I FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
Authors: LowKam, C. / Arthus-Cartier, G. / Sygusch, J.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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

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)157,2476
Polymers157,0634
Non-polymers1842
Water33,0401834
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-31 kcal/mol
Surface area52360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.477, 103.194, 84.527
Angle α, β, γ (deg.)90.00, 98.66, 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: 39265.688 Da / Num. of mol.: 4 / Mutation: K229M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Production host: Escherichia coli (E. coli) / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1834 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→35.201 Å / Num. obs: 122560 / % possible obs: 99.7 % / Redundancy: 3.6 % / Net I/σ(I): 25.13
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.43 / Num. unique all: 12223 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZAH

1zah


Resolution: 1.84→35.201 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1739 2001 1.63 %
Rwork0.1459 --
obs0.1464 122436 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→35.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11028 0 12 1834 12874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711295
X-RAY DIFFRACTIONf_angle_d1.05515311
X-RAY DIFFRACTIONf_dihedral_angle_d13.0554194
X-RAY DIFFRACTIONf_chiral_restr0.0411728
X-RAY DIFFRACTIONf_plane_restr0.0051996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8374-1.88340.24581460.20358267X-RAY DIFFRACTION96
1.8834-1.93430.24181400.19048593X-RAY DIFFRACTION100
1.9343-1.99120.22891410.17268657X-RAY DIFFRACTION100
1.9912-2.05550.19641390.17068594X-RAY DIFFRACTION100
2.0555-2.12890.19141480.15768608X-RAY DIFFRACTION100
2.1289-2.21420.20151350.15098614X-RAY DIFFRACTION100
2.2142-2.31490.16321430.15128635X-RAY DIFFRACTION100
2.3149-2.43690.1881470.14518591X-RAY DIFFRACTION100
2.4369-2.58960.17781430.14348639X-RAY DIFFRACTION100
2.5896-2.78940.18011420.14478660X-RAY DIFFRACTION100
2.7894-3.070.16711450.14778615X-RAY DIFFRACTION100
3.07-3.51390.18011440.14058671X-RAY DIFFRACTION100
3.5139-4.42580.14251420.12148666X-RAY DIFFRACTION100
4.4258-35.20710.14091460.1368625X-RAY DIFFRACTION98

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