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- PDB-1dos: STRUCTURE OF FRUCTOSE-BISPHOSPHATE ALDOLASE -

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Basic information

Entry
Database: PDB / ID: 1dos
TitleSTRUCTURE OF FRUCTOSE-BISPHOSPHATE ALDOLASE
ComponentsALDOLASE CLASS II
KeywordsLYASE / CLASSII FRUCTOSE 1 / 6-BISPHOSPHATE ALDOLASE / GLYCOLYSIS
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Fructose-bisphosphate aldolase class 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.67 Å
AuthorsBlom, N. / Tetreault, S. / Coulombe, R. / Sygusch, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase.
Authors: Blom, N.S. / Tetreault, S. / Coulombe, R. / Sygusch, J.
#1: Journal: To be Published
Title: Enhanced Electron Density Envelopes by Extended Solvent Definition
Authors: Blom, N. / Sygusch, J.
History
DepositionJun 24, 1996Processing site: BNL
Revision 1.0Jul 7, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: ALDOLASE CLASS II
B: ALDOLASE CLASS II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2356
Polymers78,0682
Non-polymers1674
Water27,7971543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-63 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.530, 73.380, 57.800
Angle α, β, γ (deg.)90.00, 106.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALDOLASE CLASS II


Mass: 39033.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM83P33 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB71, fructose-bisphosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1543 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: free interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
20.2 M11MgCl2
30.1 MHEPES11
425-26 %PEG400012
50.2 M12MgCl2
60.1 MHEPES12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 7, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.052
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 75160 / % possible obs: 74.3 % / Num. measured all: 242370

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementResolution: 1.67→10 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5883 8 %RANDOM
Rwork0.171 ---
obs0.171 73116 87.4 %-
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.29 Å2
2--0.11 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.67→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6688 0 4 1543 8235
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_deg2.091
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.86
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.209
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: 1.67→1.76 Å
RfactorNum. reflection% reflection
Rfree0.312 577 9.8 %
Rwork0.303 6982 -
obs--63.7 %
Software
*PLUS
Name: X-PLOR / 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_deg21.86
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.209

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