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- PDB-1wbh: Crystal structure of the E45N mutant from KDPG aldolase from Esch... -

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Basic information

Entry
Database: PDB / ID: 1wbh
TitleCrystal structure of the E45N mutant from KDPG aldolase from Escherichia coli
ComponentsKHG/KDPG ALDOLASE
KeywordsLYASE / ALDOLASE / KDPG ALDOLASE / ESCHERICHIA COLI
Function / homology
Function and homology information


(4S)-4-hydroxy-2-oxoglutarate aldolase / 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 / metabolic process / 2-dehydro-3-deoxy-phosphogluconate aldolase activity ...(4S)-4-hydroxy-2-oxoglutarate aldolase / 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 / metabolic process / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / aldehyde-lyase activity / identical protein binding / membrane / cytoplasm / 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
PHOSPHATE ION / KHG/KDPG aldolase / KHG/KDPG aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFullerton, S.W.B. / Merkel, A.B. / Naismith, J.H.
CitationJournal: Bioorg.Med.Chem. / Year: 2006
Title: Mechanism of the Class I Kdpg Aldolase.
Authors: Fullerton, S.W.B. / Griffiths, J.S. / Merkel, A.B. / Cheriyan, M. / Wymer, N.J. / Hutchins, M.J. / Fierke, C.A. / Toone, E.J. / Naismith, J.H.
History
DepositionNov 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KHG/KDPG ALDOLASE
B: KHG/KDPG ALDOLASE
C: KHG/KDPG ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4637
Polymers67,0833
Non-polymers3804
Water12,971720
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.492, 84.244, 132.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.551184, 0.601424, -0.578348), (-0.337983, -0.472801, -0.813773), (-0.762866, 0.64401, -0.057329)34.2519, -60.933, 40.955
2given(0.583962, -0.271569, -0.765009), (0.616342, -0.464983, 0.635542), (-0.528309, -0.942639, -0.104153)39.7368, 16.9328, 69.6169

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Components

#1: Protein KHG/KDPG ALDOLASE / 4-HYDROXY-2-OXOGLUTARATE ALDOLASE / 2-KETO-4-HYDROXYGLUTARATE ALDOLASE / KHG-ALDOLASE / 2-DEHYDRO-3- ...4-HYDROXY-2-OXOGLUTARATE ALDOLASE / 2-KETO-4-HYDROXYGLUTARATE ALDOLASE / KHG-ALDOLASE / 2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE / PHOSPHO-2-DEHYDRO-3-DEOXYGLUCONATE ALDOLASE / PHOSPHO-2-KETO-3-DEOXYGLUCONATE ALDOLASE / 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE


Mass: 22361.018 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PHOSPHATE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET30B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10177, UniProt: P0A955*PLUS, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 720 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE CHAIN A, B, C GLU 45 ASN

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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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growpH: 4.6
Details: 0.075M SODIUM ACETATE, 0.1M AMMONIUM SULPHATE, 27%W/V PEG4000, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 14, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 89181 / % possible obs: 99.4 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.55→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUA

1eua


Resolution: 1.55→40.16 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.05 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4409 5 %RANDOM
Rwork0.168 ---
obs0.17 82974 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 20 720 5440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9966453
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45624.671152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13315761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0321521
X-RAY DIFFRACTIONr_chiral_restr0.1040.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023473
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.22526
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23328
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2521
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6641.53233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3225061
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.08731681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4934.51392
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 335
Rwork0.165 5984

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