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Basic information

Entry
Database: PDB / ID: 2iyo
TitleStructural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition
Components6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
KeywordsOXIDOREDUCTASE / 6-PHOSPHOGLUCONATE DEHYDROGENASE / NADP / PENTOSE SHUNT / GLUCONATE UTILIZATION
Function / homology
Function and homology information


phosphogluconate 2-dehydrogenase activity / D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt, oxidative branch / NADP binding / cytosol
Similarity search - Function
6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase ...6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-PHOSPHOGLUCONIC ACID / CACODYLATE ION / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSundaramoorthy, R. / Iulek, J. / Hunter, W.N.
CitationJournal: FEBS J. / Year: 2007
Title: Crystal Structures of a Bacterial 6-Phosphogluconate Dehydrogenase Reveal Aspects of Specificity, Mechanism and Mode of Inhibition by Analogues of High-Energy Reaction Intermediates.
Authors: Sundaramoorthy, R. / Iulek, J. / Barrett, M.P. / Bidet, O. / Ruda, G.F. / Gilbert, I.H. / Hunter, W.N.
History
DepositionJul 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9143
Polymers52,5011
Non-polymers4132
Water5,639313
1
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules

A: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8296
Polymers105,0022
Non-polymers8264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)60.582, 60.582, 243.128
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING


Mass: 52501.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Strain: MG1363 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96789, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.3 Å3/Da / Density % sol: 46 %
Description: DATA WERE COLLECTED USING OSCILLATION PHOTOGRAPH
Crystal growpH: 7.2
Details: 25% PEG 3350, 300MM AMMONIUM ACCETATE, 0.1M SODIUM CACODYLATE, pH 7.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 5, 2004 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 19558 / % possible obs: 96 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.7 / % possible all: 75

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PGD

2pgd


Resolution: 2.4→19.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.445 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1003 5.1 %RANDOM
Rwork0.159 ---
obs0.162 18555 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 22 313 4007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.975090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89324.74173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75715651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3451519
X-RAY DIFFRACTIONr_chiral_restr0.0840.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022842
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21846
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22579
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.2140
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.481.52381
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82923720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.20431565
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9784.51370
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 50
Rwork0.187 1009

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