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- PDB-1zen: CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE -

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Basic information

Entry
Database: PDB / ID: 1zen
TitleCLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
ComponentsCLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
KeywordsLYASE / ALDEHYDE / 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
Fructose-bisphosphate aldolase class 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsCooper, S.J. / Leonard, G.A. / Hunter, W.N.
Citation
Journal: Structure / Year: 1996
Title: The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding active site embedded in a familiar fold.
Authors: Cooper, S.J. / Leonard, G.A. / McSweeney, S.M. / Thompson, A.W. / Naismith, J.H. / Qamar, S. / Plater, A. / Berry, A. / Hunter, W.N.
#1: Journal: Protein Sci. / Year: 1996
Title: Identification of Arginine 331 as an Important Active Site Residue in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli
Authors: Qamar, S. / Marsh, K. / Berry, A.
#2: Journal: FEBS Lett. / Year: 1993
Title: Identification of Zinc Binding Ligands in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli
Authors: Berry, A. / Marshall, K.E.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Initiating a Crystallographic Study of a Class II Fructose-1,6-Bisphosphate Aldolase
Authors: Naismith, J.H. / Ferrara, J.D. / Bailey, S. / Marshall, K. / Dauter, Z. / Wilson, K.S. / Habash, J. / Harrop, S.J. / Berry, A.J. / Hunter, W.N.
History
DepositionJul 8, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1913
Polymers39,0601
Non-polymers1312
Water1,26170
1
A: CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
hetero molecules

A: CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3826
Polymers78,1202
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5140 Å2
ΔGint-107 kcal/mol
Surface area27480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.360, 78.360, 290.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE


Mass: 39059.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): K12 CS520 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: Kitagawa, Y., (1995) Acta Cryst. D., 51, 833.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
2100 mMTris-HCl1drop
310-20 %(w/v)PEG40001drop
40.02-0.3 M1dropMgCl2
5PEG40001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionNum. obs: 18922 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.071
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 98 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→6 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.326 -9.84 %
Rwork0.243 --
obs0.243 14290 82.3 %
Displacement parametersBiso mean: 35.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 2 70 2638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.0115
X-RAY DIFFRACTIONx_mcangle_it2.4035
X-RAY DIFFRACTIONx_scbond_it0.0177
X-RAY DIFFRACTIONx_scangle_it1.2227
LS refinement shellResolution: 2.5→2.6 Å
RfactorNum. reflection% reflection
Rwork0.0439 942 -
obs--43.19 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.65

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