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- PDB-1ado: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM RABBIT MUSCLE -

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Basic information

Entry
Database: PDB / ID: 1ado
TitleFRUCTOSE 1,6-BISPHOSPHATE ALDOLASE FROM RABBIT MUSCLE
ComponentsALDOLASE
KeywordsLYASE / ALDOLASE / LYASE (ALDEHYDE) / SCHIFF BASE / GLYCOLYSIS
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
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBlom, N.S. / Sygusch, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Product binding and role of the C-terminal region in class I D-fructose 1,6-bisphosphate aldolase.
Authors: Blom, N. / Sygusch, J.
#1: Journal: To be Published
Title: Enhanced Electron Density Envelopes by Extended Solvent Definition
Authors: Blom, N.S. / Sygusch, J.
History
DepositionDec 2, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALDOLASE
B: ALDOLASE
C: ALDOLASE
D: ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5478
Polymers157,0154
Non-polymers5324
Water59,2333288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-63 kcal/mol
Surface area53980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.880, 57.470, 85.030
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ALDOLASE


Mass: 39253.637 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3288 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growpH: 7.5
Details: RABBIT MUSCLE ALDOLASE WAS CRYSTALLIZED FROM A 42% SATURATED AMMONIUM SULFATE SOLUTION, pH 7.5
Crystal grow
*PLUS
pH: 7.3 / Method: unknown / Details: Eagles, P. A., (1969) J. Mol. Biol., 45, 533-544
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
20.1 Mtriethanolamine-hydrochloride11
35 mMEDTA11
444-49 %satammonium sulfate11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1991
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→12 Å / Num. obs: 103662 / % possible obs: 85.2 % / Observed criterion σ(I): 1 / Rsym value: 0.056 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.286
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Rmerge(I) obs: 0.286

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE TO 2.7 ANGSTROM RESOLUTION

Resolution: 1.9→12 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.203 8287 8 %RANDOM
Rwork0.162 ---
obs0.162 103662 85.2 %-
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.7349 Å20 Å20 Å2
2--1.8477 Å20 Å2
3----0.1129 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13592 0 34 3288 16914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.718
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.89
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.222
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.29 657 8.1 %
Rwork0.262 7437 -
obs--53.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.89
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.222
LS refinement shell
*PLUS
Rfactor obs: 0.262

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