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- PDB-1eun: STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE FROM ESCH... -

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Basic information

Entry
Database: PDB / ID: 1eun
TitleSTRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE FROM ESCHERICHIA COLI
ComponentsKDPG ALDOLASE
KeywordsLYASE / 2-keto-3-deoxy-6-phosphogluconate aldolase / sulfate / trimer / beta-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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsAllard, J. / Grochulski, P. / Sygusch, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution.
Authors: Allard, J. / Grochulski, P. / Sygusch, J.
History
DepositionApr 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)67,4919
Polymers66,9153
Non-polymers5766
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-127 kcal/mol
Surface area25080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.950, 85.210, 133.690
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 natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0A955, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 320 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, Ammonium sulfate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 320K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris-HCl1reservoir
318.5 %PEG35001reservoir
40.2 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 43245 / Num. obs: 39588 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.66 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20
Reflection shellResolution: 2→2.13 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.269 / % possible all: 79.4
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 39315 / % possible obs: 94.8 % / Rmerge(I) obs: 0.075

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2→39.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 228160.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1995 5 %RANDOM
Rwork0.202 ---
obs0.202 39588 91.6 %-
all-43218 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.09 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.465 Å20 Å20 Å2
2--5.637 Å20 Å2
3---4.828 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 30 749 5475
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005617
X-RAY DIFFRACTIONc_angle_deg1.3263
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.2831.5
X-RAY DIFFRACTIONc_mcangle_it1.9582
X-RAY DIFFRACTIONc_scbond_it2.1382
X-RAY DIFFRACTIONc_scangle_it3.0062.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 277 4.9 %
Rwork0.269 5368 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ACT.PARACT.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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