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- PDB-5gk8: Structure of E.Coli fructose 1,6-bisphosphate aldolase, Acetate b... -

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Basic information

Entry
Database: PDB / ID: 5gk8
TitleStructure of E.Coli fructose 1,6-bisphosphate aldolase, Acetate bound form
ComponentsFructose-bisphosphate aldolase class 2
KeywordsLYASE / FBA Acetate bound
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Fructose-bisphosphate aldolase class 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsTran, T.H. / Huynh, K.H. / Ho, T.H. / Kang, L.W.
CitationJournal: To Be Published
Title: Structure of E.Coli fructose 1,6-bisphosphate aldolase, Acetate bound form
Authors: Tran, T.H. / Huynh, K.H. / Ho, T.H. / Kang, L.W.
History
DepositionJul 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase class 2
B: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,23713
Polymers78,3822
Non-polymers85411
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-182 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.598, 73.351, 78.269
Angle α, β, γ (deg.)90.000, 102.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructose-bisphosphate aldolase class 2 / FBPA / Fructose-1 / 6-bisphosphate aldolase / Fructose-bisphosphate aldolase class II


Mass: 39191.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fbaA, fba, fda, b2925, JW2892 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AB71, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 365 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 46.77 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium acetate, 5% fructose 1,6-bisphosphatase, 0.1 M Tris pH 7.0, and 15% PEG 4000
PH range: 5.6-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2014
RadiationMonochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49638 / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 40.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 7.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOS

1dos


Resolution: 2.002→36.605 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.1998 1999 4.03 %
Rwork0.1606 --
obs0.1622 49606 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.78 Å2 / Biso mean: 25.0623 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 2.002→36.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 43 354 5525
Biso mean--37.99 31.56 -
Num. residues----663

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