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- PDB-1wa3: Mechanism of the Class I KDPG aldolase -

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Basic information

Entry
Database: PDB / ID: 1wa3
TitleMechanism of the Class I KDPG aldolase
Components2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
KeywordsLYASE / KDPG / PYRUVATE
Function / homology
Function and homology information


D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity
Similarity search - Function
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
PYRUVIC ACID / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFullerton, S.W.B. / Griffiths, J.S. / Merkel, A.B. / Wymer, N.J. / Hutchins, M.J. / Fierke, C.A. / Toone, E.J. / 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
DepositionOct 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 23, 2013Group: Derived calculations / Other / Structure summary
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
B: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
C: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
D: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
E: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
F: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,70718
Polymers133,6036
Non-polymers1,10512
Water5,513306
1
A: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
B: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
C: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3549
Polymers66,8013
Non-polymers5526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-72.3 kcal/mol
Surface area23550 Å2
MethodPISA
2
D: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
E: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
F: 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3549
Polymers66,8013
Non-polymers5526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-74.5 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.600, 101.100, 124.600
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE / 4-HYDROXY-2-OXOGLUTARATE ALDOLASE / 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE / 4-HYDROXY-2- ...4-HYDROXY-2-OXOGLUTARATE ALDOLASE / 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE / 4-HYDROXY-2-OXOGLUTARATE ALDOLASE


Mass: 22267.123 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE FORMED WITH PYRUVATE IN THE ACTIVE SITE
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Description: DSM 3109 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WXS1, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.5 %
Crystal growpH: 4.6
Details: 0.075M SODIUM ACETATE, 0.1M AMMONIUM SULPHATE, 28%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: 0.932
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: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.9→32.97 Å / Num. obs: 309752 / % possible obs: 94.3 % / Observed criterion σ(I): 1.5 / Redundancy: 4 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3 / % possible all: 94.3

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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: 1.9→32.44 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.84 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3900 5 %RANDOM
Rwork0.193 ---
obs0.195 73594 94 %-
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: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9203 0 60 306 9569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229437
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.98312705
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24451205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80525.179336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.334151738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3711524
X-RAY DIFFRACTIONr_chiral_restr0.1430.21463
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.24506
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26487
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2450
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.2134
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3950.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1121.56172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59929687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.77533608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4934.53018
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: 1.9→1.94 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.301 201 -
Rwork0.214 4320 -
obs--92.1 %
Refinement TLS params.

T11: 0.0036 Å2 / T23: 0.0076 Å2 / T33: 0.0176 Å2 / Method: refined / Origin x: 16.556 Å / Origin y: 33.747 Å / Origin z: 36.601 Å / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T12 (Å2)T13 (Å2)T22 (Å2)
10.06320.05290.04960.14820.28820.6474-0.0031-0.0344-0.001-0.0791-0.00410.0192-0.16520.01310.00720.00770.00650.0234
20.06770.09910.05090.54720.5790.69930.0118-0.0125-0.03330.03450.0571-0.02370.01390.1052-0.06890.00770.00650.0234
30.10590.2136-0.00122.5720.41660.0820.2247-0.0699-0.02540.8109-0.0905-0.22050.5003-0.0246-0.13420.00770.00630.0234
40.22610.44860.53030.89711.00171.60820.08570.0066-0.06920.25230.2294-0.34730.41780.0943-0.31510.00740.00650.0235
50.11050.03540.19820.20550.31030.66920.1058-0.053-0.02740.0002-0.056-0.0034-0.0317-0.0255-0.04990.00760.00650.0234
60.40980.10150.16940.66120.40960.28250.04020.0173-0.17520.0131-0.0055-0.0701-0.03020.0226-0.03470.00770.00650.0234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 203
2X-RAY DIFFRACTION2B2 - 203
3X-RAY DIFFRACTION3C3 - 203
4X-RAY DIFFRACTION4D2 - 204
5X-RAY DIFFRACTION5E2 - 203
6X-RAY DIFFRACTION6F3 - 203

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