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- PDB-1mxs: Crystal structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) ald... -

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Basic information

Entry
Database: PDB / ID: 1mxs
TitleCrystal structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida.
ComponentsKDPG Aldolase
KeywordsLYASE / 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE / SULFATE / BETA-BARREL
Function / homology
Function and homology information


2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity
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
2-dehydro-3-deoxy-phosphogluconate aldolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWatanabe, L. / Bell, B.J. / Lebioda, L. / Rios-Steiner, J.L. / Tulinsky, A. / Arni, R.K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase from Pseudomonas putida.
Authors: Bell, B.J. / Watanabe, L. / Rios-Steiner, J.L. / Tulinsky, A. / Lebioda, L. / Arni, R.K.
#1: Journal: 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.
#2: Journal: 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.
#3: Journal: Biochemistry / Year: 1976
Title: The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-A resolution.
Authors: Mavridis, I.M. / Tulinsky, A.
#4: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2.8A resolution
Authors: Mavridis, I.M. / Hatada, M.H. / Tulinsky, A. / Lebioda, L.
History
DepositionOct 3, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_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

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Assembly

Deposited unit
A: KDPG Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1963
Polymers24,0041
Non-polymers1922
Water1,00956
1
A: KDPG Aldolase
hetero molecules

A: KDPG Aldolase
hetero molecules

A: KDPG Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5889
Polymers72,0113
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area5100 Å2
ΔGint-144 kcal/mol
Surface area23990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.300, 103.300, 103.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-333-

HOH

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Components

#1: Protein KDPG Aldolase / 2-dehydro-3-deoxyphosphogluconate aldolase


Mass: 24003.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria)
References: UniProt: P00885, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.82 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 296 K / Method: microdialysis / pH: 3.5
Details: ammonium sulfate, KH2PO4, pH 3.5, MICRODIALYSIS, temperature 296K
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein11
21.5 Mammonium sulfate12
30.1 M12pH3.5KH2PO4

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: Yale/MSC mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→9.98 Å / Num. obs: 9901 / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.046
Reflection shellResolution: 2.2→50 Å / Num. unique all: 9901 / Rsym value: 0.046
Reflection
*PLUS
% possible obs: 52.3 % / Num. measured all: 66178 / Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUN

1eun


Resolution: 2.2→9.98 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 525 5.3 %RANDOM
Rwork0.171 ---
obs0.171 9901 52.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9183 Å2 / ksol: 0.341747 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.2→9.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 10 56 1669
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.2→50 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 31 6 %
Rwork0.3 488 -
obs--16.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 9999 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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