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- PDB-1eua: SCHIFF BASE INTERMEDIATE IN KDPG ALDOLASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1eua
TitleSCHIFF BASE INTERMEDIATE IN KDPG ALDOLASE FROM ESCHERICHIA COLI
ComponentsKDPG ALDOLASE2-Dehydro-3-deoxy-phosphogluconate aldolase
KeywordsLYASE / BETA BARREL / TRIMER / CARBINOLAMINE
Function / homology
Function and homology information


(4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 4-hydroxy-2-oxoglutarate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase / 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
ACETATE ION / PYRUVIC ACID / 2-dehydro-3-deoxy-phosphogluconate aldolase / KHG/KDPG aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 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 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 21, 2015Group: Refinement description
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: KDPG ALDOLASE
B: KDPG ALDOLASE
C: KDPG ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,58511
Polymers66,9153
Non-polymers6708
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-55 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.410, 85.720, 133.190
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: 22304.951 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0A955, UniProt: A0A140NB38*PLUS, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
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: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→99 Å / Num. all: 45706 / Num. obs: 44409 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Biso Wilson estimate: 17.2 Å2 / Limit h max: 27 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 68 / Limit l min: 0 / Observed criterion F max: 601772.91 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.087 / Net I/σ(I): 30
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.94 % / Rmerge(I) obs: 0.293 / % possible all: 92.2
Reflection
*PLUS
% possible obs: 99.4 %
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.95→50.37 Å / Occupancy max: 1 / Occupancy min: 0.8 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2226 -RANDOM
Rwork0.201 ---
all0.243 45706 --
obs0.201 44409 97.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 51.5349 Å2 / ksol: 0.362848 e/Å3
Displacement parametersBiso mean: 32.92 Å2
Baniso -1Baniso -2Baniso -3
1--9.567 Å20 Å20 Å2
2--1.131 Å20 Å2
3---8.435 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.95→50.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 41 616 5355
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005618
X-RAY DIFFRACTIONc_angle_deg1.3154
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.3021.5
X-RAY DIFFRACTIONc_mcangle_it1.9542
X-RAY DIFFRACTIONc_scbond_it2.1511.5
X-RAY DIFFRACTIONc_scangle_it3.1052.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2pyr.parpyr.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5act.paract.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.243 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
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_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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