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- PDB-8q2i: Crystal structure of Ser33 in complex 2HG (2-hydroxyglutarate) an... -

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Basic information

Entry
Database: PDB / ID: 8q2i
TitleCrystal structure of Ser33 in complex 2HG (2-hydroxyglutarate) and Serine
ComponentsD-3-phosphoglycerate dehydrogenase 2
KeywordsCYTOSOLIC PROTEIN / Enzyme protein
Function / homology
Function and homology information


alpha-ketoglutarate reductase activity / serine family amino acid biosynthetic process / 2-oxoglutarate reductase / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / L-serine biosynthetic process / NAD binding / identical protein binding / cytoplasm
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / ACT domain profile. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...: / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / ACT domain profile. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / ACT-like domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(2R)-2-hydroxypentanedioic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SERINE / D-3-phosphoglycerate dehydrogenase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsPerrone, S. / Cifuente, J.O. / Marina, A. / Mastrella, L. / Trastoy, B. / Linster, C.L. / Guerin, M.E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
CitationJournal: To Be Published
Title: Crystal structure of Ser33 in complex 2HG (2-hydroxyglutarate) and Serine
Authors: Perrone, S. / Cifuente, J.O. / Marina, A. / Mastrella, L. / Trastoy, B. / Linster, C.L. / Guerin, M.E.
History
DepositionAug 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-3-phosphoglycerate dehydrogenase 2
B: D-3-phosphoglycerate dehydrogenase 2
C: D-3-phosphoglycerate dehydrogenase 2
D: D-3-phosphoglycerate dehydrogenase 2
E: D-3-phosphoglycerate dehydrogenase 2
F: D-3-phosphoglycerate dehydrogenase 2
G: D-3-phosphoglycerate dehydrogenase 2
H: D-3-phosphoglycerate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,68528
Polymers409,9448
Non-polymers6,74120
Water3,279182
1
A: D-3-phosphoglycerate dehydrogenase 2
B: D-3-phosphoglycerate dehydrogenase 2
C: D-3-phosphoglycerate dehydrogenase 2
D: D-3-phosphoglycerate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,19413
Polymers204,9724
Non-polymers3,2229
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25760 Å2
ΔGint-126 kcal/mol
Surface area69680 Å2
MethodPISA
2
E: D-3-phosphoglycerate dehydrogenase 2
F: D-3-phosphoglycerate dehydrogenase 2
G: D-3-phosphoglycerate dehydrogenase 2
H: D-3-phosphoglycerate dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,49115
Polymers204,9724
Non-polymers3,51811
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25000 Å2
ΔGint-127 kcal/mol
Surface area68850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.292, 112.378, 117.358
Angle α, β, γ (deg.)64.990, 66.560, 67.180
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein
D-3-phosphoglycerate dehydrogenase 2 / 3-PGDH 2 / 2-oxoglutarate reductase


Mass: 51243.039 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SER33, YIL074C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P40510, phosphoglycerate dehydrogenase, 2-oxoglutarate reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-2HG / (2R)-2-hydroxypentanedioic acid


Mass: 148.114 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate 0.1 M Bis-Tris propane 8.5 20 % w/v PEG 3350 7.4 mg/ml of protein in 25 mM Tris pH=7.5 and 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.51→20.02 Å / Num. obs: 146160 / % possible obs: 97.21 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 10.55
Reflection shellResolution: 2.51→2.6 Å / Num. unique obs: 14197 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→20.02 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2525 --
Rwork0.2357 --
obs-7403 97.03 %
Refinement stepCycle: LAST / Resolution: 2.51→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26733 0 448 182 27363

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