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- PDB-1fwr: CRYSTAL STRUCTURE OF KDPG ALDOLASE DOUBLE MUTANT K133Q/T161K -

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Basic information

Entry
Database: PDB / ID: 1fwr
TitleCRYSTAL STRUCTURE OF KDPG ALDOLASE DOUBLE MUTANT K133Q/T161K
ComponentsKDPG ALDOLASE2-Dehydro-3-deoxy-phosphogluconate aldolase
KeywordsLYASE / TIM barrel
Function / homology
Function and homology information


(4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase / 4-hydroxy-2-oxoglutarate aldolase activity / oxo-acid-lyase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / metabolic process / membrane / identical protein binding / 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: 2.7 Å
AuthorsNaismith, J.H. / Buchanan, L.V.
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 24, 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 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)67,5726
Polymers66,9963
Non-polymers5763
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-25 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.87, 84.5, 135.013
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 / 2-Dehydro-3-deoxy-phosphogluconate aldolase


Mass: 22331.977 Da / Num. of mol.: 3 / Mutation: K133Q, T161K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A955, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 6K 20%, 0.075M citric acid, 30% sucrose, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
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: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→67 Å / Num. all: 57991 / Num. obs: 57991 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.256 / Num. unique all: 8553 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 67 Å / Num. obs: 17894 / % possible obs: 99.8 %
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 100 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.7→67 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.276 2899 same 5% as for 1FQ0
Rwork0.238 --
all0.238 203083 -
obs0.238 57991 -
Refinement stepCycle: LAST / Resolution: 2.7→67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 39 137 4880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.013
X-RAY DIFFRACTIONc_bond_d0.0063
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 67 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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