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- PDB-2ot1: Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex ... -

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Basic information

Entry
Database: PDB / ID: 2ot1
TitleFructose-1,6-bisphosphate aldolase from rabbit muscle in complex with naphthol AS-E phosphate, a competitive inhibitor
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / glycolysis / competitive inhibition / hydrophobic pocket
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / I band / M 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
Chem-N3P / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSt-Jean, M. / Izard, T. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: A hydrophobic pocket in the active site of glycolytic aldolase mediates interactions with wiskott-Aldrich syndrome protein.
Authors: St-Jean, M. / Izard, T. / Sygusch, J.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)158,5668
Polymers157,0554
Non-polymers1,5114
Water33,5621863
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13580 Å2
ΔGint-49 kcal/mol
Surface area48740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.780, 103.445, 83.601
Angle α, β, γ (deg.)90.00, 98.66, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the homotetramer found in the asymmetric unit

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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: Chemical
ChemComp-N3P / N-(4-CHLOROPHENYL)-3-(PHOSPHONOOXY)NAPHTHALENE-2-CARBOXAMIDE


Mass: 377.716 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H13ClNO5P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1863 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 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: X8C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 85601 / Num. obs: 85601 / % possible obs: 95.3 % / Redundancy: 3.6 % / Rsym value: 0.054 / Net I/σ(I): 26.3
Reflection shellResolution: 2.05→2.14 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 8047 / Rsym value: 0.162 / % possible all: 72.1

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZAH
Resolution: 2.05→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.197 8166 -random
Rwork0.149 ---
all-85601 --
obs-81422 91.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.478 Å20 Å22.875 Å2
2---5.515 Å20 Å2
3----0.963 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10764 0 100 1863 12727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.21
LS refinement shellResolution: 2.05→2.14 Å
RfactorNum. reflection% reflection
Rfree0.215 707 -
Rwork0.169 --
obs-7016 62.9 %

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