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- PDB-5uq9: Crystal structure of 6-phosphogluconate dehydrogenase with ((4R,5... -

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Basic information

Entry
Database: PDB / ID: 5uq9
TitleCrystal structure of 6-phosphogluconate dehydrogenase with ((4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl)methyl dihydrogen phosphate
Components6-phosphogluconate dehydrogenase, decarboxylating
KeywordsOXIDOREDUCTASE / Rossmann fold / Pentose phosphate pathway / Dehydrogenase
Function / homology
Function and homology information


D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose biosynthetic process / pentose-phosphate shunt, oxidative branch / Pentose phosphate pathway / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / NADP binding / extracellular exosome ...D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose biosynthetic process / pentose-phosphate shunt, oxidative branch / Pentose phosphate pathway / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / NADP binding / extracellular exosome / nucleus / cytosol
Similarity search - Function
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 ...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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8HS / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsLeonard, P.G.
CitationJournal: Cell Rep / Year: 2019
Title: Functional Genomics Reveals Synthetic Lethality between Phosphogluconate Dehydrogenase and Oxidative Phosphorylation.
Authors: Sun, Y. / Bandi, M. / Lofton, T. / Smith, M. / Bristow, C.A. / Carugo, A. / Rogers, N. / Leonard, P. / Chang, Q. / Mullinax, R. / Han, J. / Shi, X. / Seth, S. / Meyers, B.A. / Miller, M. / ...Authors: Sun, Y. / Bandi, M. / Lofton, T. / Smith, M. / Bristow, C.A. / Carugo, A. / Rogers, N. / Leonard, P. / Chang, Q. / Mullinax, R. / Han, J. / Shi, X. / Seth, S. / Meyers, B.A. / Miller, M. / Miao, L. / Ma, X. / Feng, N. / Giuliani, V. / Geck Do, M. / Czako, B. / Palmer, W.S. / Mseeh, F. / Asara, J.M. / Jiang, Y. / Morlacchi, P. / Zhao, S. / Peoples, M. / Tieu, T.N. / Warmoes, M.O. / Lorenzi, P.L. / Muller, F.L. / DePinho, R.A. / Draetta, G.F. / Toniatti, C. / Jones, P. / Heffernan, T.P. / Marszalek, J.R.
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: 6-phosphogluconate dehydrogenase, decarboxylating
E: 6-phosphogluconate dehydrogenase, decarboxylating
F: 6-phosphogluconate dehydrogenase, decarboxylating
G: 6-phosphogluconate dehydrogenase, decarboxylating
H: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,3799
Polymers430,1088
Non-polymers2711
Water0
1
A: 6-phosphogluconate dehydrogenase, decarboxylating
B: 6-phosphogluconate dehydrogenase, decarboxylating


Theoretical massNumber of molelcules
Total (without water)107,5272
Polymers107,5272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-75 kcal/mol
Surface area33950 Å2
MethodPISA
2
C: 6-phosphogluconate dehydrogenase, decarboxylating
D: 6-phosphogluconate dehydrogenase, decarboxylating


Theoretical massNumber of molelcules
Total (without water)107,5272
Polymers107,5272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-77 kcal/mol
Surface area34230 Å2
MethodPISA
3
E: 6-phosphogluconate dehydrogenase, decarboxylating
F: 6-phosphogluconate dehydrogenase, decarboxylating
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7983
Polymers107,5272
Non-polymers2711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-80 kcal/mol
Surface area33520 Å2
MethodPISA
4
G: 6-phosphogluconate dehydrogenase, decarboxylating
H: 6-phosphogluconate dehydrogenase, decarboxylating


Theoretical massNumber of molelcules
Total (without water)107,5272
Polymers107,5272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-71 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.311, 164.930, 133.199
Angle α, β, γ (deg.)90.000, 91.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
6-phosphogluconate dehydrogenase, decarboxylating /


Mass: 53763.504 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGD, PGDH / Production host: Escherichia coli (E. coli)
References: UniProt: P52209, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Chemical ChemComp-8HS / [(4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl dihydrogen phosphate


Mass: 271.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14NO8P

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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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 13% (w/v) PEG 3350, 10.0% (v/v) ethylene glycol / Temp details: Room temp

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3→87.283 Å / Num. obs: 75282 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 60.05 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.076 / Rrim(I) all: 0.144 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.060.8860.5020.5491.04599.9
15-87.280.0450.9940.0280.05397.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.78 Å87.28 Å
Translation7.78 Å87.28 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.56phasing
PHENIX1.10.1.2155refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JKV

2jkv


Resolution: 3→87.283 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.13
RfactorNum. reflection% reflection
Rfree0.2717 3909 5.2 %
Rwork0.2169 --
obs0.2198 75244 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.42 Å2 / Biso mean: 59.684 Å2 / Biso min: 16.59 Å2
Refinement stepCycle: final / Resolution: 3→87.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29075 0 17 0 29092
Biso mean--76.82 --
Num. residues----3746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229680
X-RAY DIFFRACTIONf_angle_d0.41940005
X-RAY DIFFRACTIONf_chiral_restr0.0374344
X-RAY DIFFRACTIONf_plane_restr0.0035167
X-RAY DIFFRACTIONf_dihedral_angle_d11.44317644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.03660.39411410.330425532694100
3.0366-3.07510.36191310.315524982629100
3.0751-3.11550.34531410.302425722713100
3.1155-3.15820.37591360.296825242660100
3.1582-3.20340.39031610.287825002661100
3.2034-3.25120.31251300.275825442674100
3.2512-3.3020.33381160.270625582674100
3.302-3.35610.30651330.256925862719100
3.3561-3.4140.34881370.253325192656100
3.414-3.47610.32051460.249125322678100
3.4761-3.54290.33231370.25125352672100
3.5429-3.61520.27551360.238225572693100
3.6152-3.69390.28381120.236725642676100
3.6939-3.77980.3519980.227325962694100
3.7798-3.87430.29381210.221425452666100
3.8743-3.97910.28991520.209925572709100
3.9791-4.09610.23741290.225292658100
4.0961-4.22840.27431450.197825692714100
4.2284-4.37950.22391420.192725412683100
4.3795-4.55480.24871600.185625292689100
4.5548-4.76210.25421710.183325092680100
4.7621-5.01310.25041120.185425762688100
5.0131-5.32720.2271640.19625492713100
5.3272-5.73840.2421470.205825372684100
5.7384-6.31580.25391390.197425732712100
6.3158-7.22930.26231400.205325612701100
7.2293-9.10660.22891670.18125362703100
9.1066-87.32030.22331650.18122586275199

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