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- PDB-2ot0: Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex ... -

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Basic information

Entry
Database: PDB / ID: 2ot0
TitleFructose-1,6-bisphosphate aldolase from rabbit muscle in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein
Components
  • Fructose-bisphosphate aldolase A
  • Wiskott-Aldrich syndrome protein C-terminal peptide
KeywordsLYASE / complex / glycolysis / actin dynamics / hydrophobic pocket / WASp
Function / homology
Function and homology information


regulation of T cell antigen processing and presentation / regulation of actin polymerization or depolymerization / Cdc42 protein signal transduction / GTPase regulator activity / negative regulation of Arp2/3 complex-mediated actin nucleation / actin filament-based movement / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / negative regulation of cell motility / actin polymerization or depolymerization ...regulation of T cell antigen processing and presentation / regulation of actin polymerization or depolymerization / Cdc42 protein signal transduction / GTPase regulator activity / negative regulation of Arp2/3 complex-mediated actin nucleation / actin filament-based movement / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / negative regulation of cell motility / actin polymerization or depolymerization / regulation of stress fiber assembly / regulation of lamellipodium assembly / I band / M band / vesicle membrane / negative regulation of stress fiber assembly / endosomal transport / RHOJ GTPase cycle / phospholipase binding / CDC42 GTPase cycle / Generation of second messenger molecules / epidermis development / RHO GTPases Activate WASPs and WAVEs / positive regulation of double-strand break repair via homologous recombination / phagocytic vesicle / RAC1 GTPase cycle / actin filament polymerization / T cell activation / actin filament / glycolytic process / FCGR3A-mediated phagocytosis / defense response / small GTPase binding / cellular response to type II interferon / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / blood coagulation / actin cytoskeleton / cell-cell junction / site of double-strand break / actin binding / protein-containing complex assembly / protein homotetramerization / positive regulation of cell migration / immune response / protein kinase binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. ...Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. / Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Aldolase class I / PH-like domain superfamily / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A / Actin nucleation-promoting factor WAS
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
Revision 1.3Aug 30, 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
E: Wiskott-Aldrich syndrome protein C-terminal peptide
F: Wiskott-Aldrich syndrome protein C-terminal peptide
G: Wiskott-Aldrich syndrome protein C-terminal peptide
H: Wiskott-Aldrich syndrome protein C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)164,1858
Polymers164,1858
Non-polymers00
Water32,4451801
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.084, 56.705, 156.188
Angle α, β, γ (deg.)90.00, 97.78, 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: Protein/peptide
Wiskott-Aldrich syndrome protein C-terminal peptide / WASp


Mass: 1782.553 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The sequence of the peptide occurs naturally in human Wiskott-Aldrich syndrome protein
References: UniProt: P42768
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1801 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, MgCl2, PEG 550 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorDate: Jun 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 91889 / Num. obs: 91889 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rsym value: 0.105 / Net I/σ(I): 13.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 13046 / Rsym value: 0.459 / % possible all: 99.9

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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

1zah


Resolution: 2.05→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2 7885 -random
Rwork0.152 ---
all-91889 --
obs-78066 84.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.806 Å20 Å21.79 Å2
2---8.518 Å20 Å2
3---4.713 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10933 0 0 1801 12734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.23
LS refinement shellResolution: 2.05→2.16 Å
RfactorNum. reflection% reflection
Rfree0.245 859 -
Rwork0.196 --
obs-8507 65 %

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