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- PDB-1fq0: KDPG ALDOLASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1fq0
TitleKDPG ALDOLASE FROM ESCHERICHIA COLI
ComponentsKDPG ALDOLASE
KeywordsLYASE / Aldolase / TIM Barrel
Function / homology
Function and homology information


(4S)-4-hydroxy-2-oxoglutarate aldolase / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / Entner-Doudoroff pathway through 6-phosphogluconate / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / aldehyde-lyase activity ...(4S)-4-hydroxy-2-oxoglutarate aldolase / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / Entner-Doudoroff pathway through 6-phosphogluconate / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / aldehyde-lyase activity / identical protein binding / membrane / cytosol
Similarity search - Function
KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / KHG/KDPG aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsNaismith, J.H.
CitationJournal: Structure / Year: 2001
Title: Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
Authors: Wymer, N. / Buchanan, L.V. / Henderson, D. / Mehta, N. / Botting, C.H. / Pocivavsek, L. / Fierke, C.A. / Toone, E.J. / Naismith, J.H.
History
DepositionSep 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Advisory / Data collection
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: KDPG ALDOLASE
B: KDPG ALDOLASE
C: KDPG ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4916
Polymers66,9153
Non-polymers5763
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-25 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.200, 77.790, 146.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KDPG ALDOLASE


Mass: 22304.951 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET-28B / Production host: Escherichia coli (E. coli)
References: UniProt: P0A955, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 6000, citric acid, sucrose, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.5K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Details: Buchanan, L.Vl., (1999) Acta Crystallogr., D55, 1946.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl1drop
23 mg/mlprotein1drop
34 mMdithiothreitol1drop
420 %PEG60001reservoir
50.075 Mcitric acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 148386 / Num. obs: 31186 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.164 / Num. unique all: 1380 / % possible all: 38.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. obs: 27601 / % possible obs: 94 % / Redundancy: 5.1 % / Num. measured all: 148386 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.26 Å / Lowest resolution: 2.37 Å / % possible obs: 80 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 4

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1559 5 %5%
Rwork0.195 ---
all0.198 31186 --
obs0.195 477520 85.3 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 39 508 5245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.86
X-RAY DIFFRACTIONc_bond_d0.017
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Highest resolution: 2.1 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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