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- PDB-2p4q: Crystal Structure Analysis of Gnd1 in Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 2p4q
TitleCrystal Structure Analysis of Gnd1 in Saccharomyces cerevisiae
Components6-phosphogluconate dehydrogenase, decarboxylating 1
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


Pentose phosphate pathway / D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt, oxidative branch / NADP binding / cellular response to oxidative stress / mitochondrion / cytoplasm / 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
CITRATE ANION / 6-phosphogluconate dehydrogenase, decarboxylating 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsHe, W. / Wang, Y. / Liu, W. / Zhou, C.Z.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1
Authors: He, W. / Wang, Y. / Liu, W. / Zhou, C.Z.
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase, decarboxylating 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0013
Polymers54,6231
Non-polymers3782
Water3,819212
1
A: 6-phosphogluconate dehydrogenase, decarboxylating 1
hetero molecules

A: 6-phosphogluconate dehydrogenase, decarboxylating 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0036
Polymers109,2462
Non-polymers7564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area12710 Å2
ΔGint-78 kcal/mol
Surface area32910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.261, 147.261, 114.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 6-phosphogluconate dehydrogenase, decarboxylating 1


Mass: 54623.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: GND1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta(DE3)
References: UniProt: P38720, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.28 Å3/Da / Density % sol: 62.47 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.28M tri-Sodium Citrate at pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2005 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.37→18.43 Å / Num. all: 29518 / Num. obs: 28662 / % possible obs: 97.1 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.37→2.52 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
AUTOMARdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PGP.pdb

1pgp


Resolution: 2.37→18.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2737745.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1474 5 %RANDOM
Rwork0.211 ---
obs0.211 27229 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.703 Å2 / ksol: 0.363091 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--11.09 Å2-4.72 Å20 Å2
2---11.09 Å20 Å2
3---22.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.37→18.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 26 212 3920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.44
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 265 5.4 %
Rwork0.28 4623 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2flc.paramflc.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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