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- PDB-4e21: The crystal structure of 6-phosphogluconate dehydrogenase from Ge... -

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Basic information

Entry
Database: PDB / ID: 4.0E+21
TitleThe crystal structure of 6-phosphogluconate dehydrogenase from Geobacter metallireducens
Components6-phosphogluconate dehydrogenase (Decarboxylating)
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt / NADP binding
Similarity search - Function
6-phosphogluconate dehydrogenase, YqeC-type / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 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 dehydrogenase, YqeC-type / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 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
6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsZhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: The crystal structure of 6-phosphogluconate dehydrogenase from Geobacter metallireducens
Authors: Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S.
History
DepositionMar 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)79,8524
Polymers79,6162
Non-polymers2362
Water3,189177
1
A: 6-phosphogluconate dehydrogenase (Decarboxylating)
B: 6-phosphogluconate dehydrogenase (Decarboxylating)
hetero molecules

A: 6-phosphogluconate dehydrogenase (Decarboxylating)
B: 6-phosphogluconate dehydrogenase (Decarboxylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7048
Polymers159,2314
Non-polymers4734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area28440 Å2
ΔGint-173 kcal/mol
Surface area44460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.297, 184.832, 93.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein 6-phosphogluconate dehydrogenase (Decarboxylating)


Mass: 39807.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (bacteria) / Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: Gmet_2620 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q39SD5, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M Bis-tris pH 5.5, 45% v/v (+/-)-2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9788 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 38644 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 26.14 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.33
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.5 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.301→41.715 Å / SU ML: 0.31 / Isotropic thermal model: Isotropic / σ(F): 0.04 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 1867 5.1 %
Rwork0.1952 --
obs0.1975 36608 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.772 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0324 Å2-0 Å20 Å2
2---12.7131 Å2-0 Å2
3---9.6808 Å2
Refinement stepCycle: LAST / Resolution: 2.301→41.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 16 177 5003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014904
X-RAY DIFFRACTIONf_angle_d1.1876622
X-RAY DIFFRACTIONf_dihedral_angle_d18.6961779
X-RAY DIFFRACTIONf_chiral_restr0.077721
X-RAY DIFFRACTIONf_plane_restr0.005872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3006-2.36280.26741270.22572323X-RAY DIFFRACTION83
2.3628-2.43230.28131270.21972427X-RAY DIFFRACTION85
2.4323-2.51080.26861220.21822521X-RAY DIFFRACTION88
2.5108-2.60050.2791440.21212544X-RAY DIFFRACTION90
2.6005-2.70460.28761280.20622577X-RAY DIFFRACTION90
2.7046-2.82770.22121520.20622655X-RAY DIFFRACTION93
2.8277-2.97670.26991440.19752671X-RAY DIFFRACTION95
2.9767-3.16320.24821310.19482768X-RAY DIFFRACTION96
3.1632-3.40730.22461700.18322707X-RAY DIFFRACTION95
3.4073-3.750.2111500.16962831X-RAY DIFFRACTION98
3.75-4.29220.17581510.16162849X-RAY DIFFRACTION99
4.2922-5.40580.22581510.17432887X-RAY DIFFRACTION99
5.4058-41.72160.26991700.22772981X-RAY DIFFRACTION98

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