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- PDB-2zya: Dimeric 6-phosphogluconate dehydrogenase complexed with 6-phospho... -

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Basic information

Entry
Database: PDB / ID: 2zya
TitleDimeric 6-phosphogluconate dehydrogenase complexed with 6-phosphogluconate
Components6-phosphogluconate dehydrogenase, decarboxylating
KeywordsOXIDOREDUCTASE / NADP / pentose phosphate pathway / 6-phosphogluconate dehydrogenase / 6-phosphogluconate / Gluconate utilization / Pentose shunt
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / organic acid catabolic process / D-gluconate metabolic process / pentose-phosphate shunt, oxidative branch / pentose-phosphate shunt / guanosine tetraphosphate binding / NADP binding / protein homodimerization activity / identical protein 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 / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, Y.-Y. / Ko, T.-P. / Lo, L.-P. / Lin, C.-H. / Wang, A.H.-J.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism
Authors: Chen, Y.-Y. / Ko, T.-P. / Chen, W.-H. / Lo, L.-P. / Lin, C.-H. / Wang, A.H.-J.
History
DepositionJan 19, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6384
Polymers106,0852
Non-polymers5522
Water25,1671397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-88 kcal/mol
Surface area32850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.004, 108.718, 133.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 6-phosphogluconate dehydrogenase, decarboxylating


Mass: 53042.723 Da / Num. of mol.: 2 / Mutation: Y378C
Source method: isolated from a genetically manipulated source
Details: Specific mutation Y378C / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: gnd / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P00350, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1397 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1M trisodium citrate dihrdrate, 0.5M ammonium acetate, 6-7% PEG 3350, 17-18% PEG 4000, 3mM 6-phosphogluconate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2006 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 131280 / Num. obs: 126816 / % possible obs: 96.6 % / Redundancy: 6.12 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 38
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.56 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.3 / Num. unique all: 12125 / % possible all: 93.4

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1pgp

1pgp


Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 6192 -RANDOM
Rwork0.1534 ---
all0.1548 122527 --
obs0.1548 116335 93.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7212 0 34 1397 8643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.77637
X-RAY DIFFRACTIONc_bond_d0.018429
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.0265
RfactorNum. reflection% reflection
Rfree0.2314 582 -
Rwork0.2049 --
obs-10934 84.42 %

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