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Basic information

Entry
Database: PDB / ID: 2iyp
Titleproduct rup
Components6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
KeywordsOXIDOREDUCTASE / 6-PHOSPHOGLUCONATE DEHYDROGENASE / NADP / PENTOSE SHUNT / GLUCONATE UTILIZATION
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / D-gluconate metabolic process / pentose-phosphate shunt / NADP binding
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
RIBULOSE-5-PHOSPHATE / ADENOSINE-2'-5'-DIPHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.79 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 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7467
Polymers157,9183
Non-polymers1,8284
Water7,638424
1
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6795
Polymers105,2792
Non-polymers1,4013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules

C: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1334
Polymers105,2792
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)71.062, 105.061, 240.484
Angle α, β, γ (deg.)90.00, 98.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 469
2114B1 - 469
3114C1 - 469

NCS oper:
IDCodeMatrixVector
1given(0.6025, -0.7615, -0.2391), (-0.757, -0.6401, 0.1313), (-0.2531, 0.1019, -0.9621)27.56, 5.524, 157.9
2given(-0.36, 0.9125, 0.1942), (-0.9137, -0.3869, 0.1246), (0.1888, -0.1326, 0.973)11.58, 5.664, 79.41

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Components

#1: Protein 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING


Mass: 52639.359 Da / Num. of mol.: 3
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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#4: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.74 Å3/Da / Density % sol: 54.74 %
Description: DATA WERE COLLECTED USING THE OSCILLATION PHOTOGRAPH
Crystal growpH: 7.2
Details: 25% PEG 3350, 0.1M SODIUM CACODYLATE, 300MM AMMONIUM ACETATE, 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 IMAGE PLATE / Detector: IMAGE PLATE / Date: May 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 39483 / % possible obs: 90.7 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→29.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.877 / SU B: 14.954 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1979 5 %RANDOM
Rwork0.179 ---
obs0.182 37504 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.79→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11015 0 116 424 11555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.97815426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32251416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88124.761523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.795151969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5231557
X-RAY DIFFRACTIONr_chiral_restr0.090.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028605
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.25996
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.27866
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2602
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.2133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5071.57139
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.718211185
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.96334708
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5564.54235
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3635 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional1.160.5
2Bmedium positional0.680.5
3Cmedium positional0.680.5
1Amedium thermal0.672
2Bmedium thermal0.512
3Cmedium thermal0.562
LS refinement shellResolution: 2.79→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 127
Rwork0.269 2405

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