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- PDB-8pin: Crystal structure of Ser33 -

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Basic information

Entry
Database: PDB / ID: 8pin
TitleCrystal structure of Ser33
Components
  • D-3-phosphoglycerate dehydrogenase 2
  • Poli-ALA
KeywordsCYTOSOLIC PROTEIN
Function / homology
Function and homology information


: / 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 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / HYDROGENPHOSPHATE ION / D-3-phosphoglycerate dehydrogenase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 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
Authors: Perrone, S. / Cifuentes, J.O. / Marina, A. / Mastrella, L. / Trastoy, B. / Linster, C. / Guerin, M.E.
History
DepositionJun 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)190,73715
Polymers187,6997
Non-polymers3,0388
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.160, 148.520, 161.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 51 through 56 and (name N...
d_2ens_1(chain "B" and ((resid 51 through 66 and (name N...
d_3ens_1(chain "C" and ((resid 51 through 66 and (name N...
d_4ens_1(chain "D" and ((resid 51 through 56 and (name N...
d_1ens_2chain "F"
d_2ens_2chain "G"
d_3ens_2chain "H"

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.955478584114, -0.0200789070611, 0.294376481382), (0.149599403012, -0.892906718534, 0.424661760246), (0.254323993988, 0.449793763283, 0.85615703968)0.932850648377, 123.508952228, -29.6435065544
2given(-0.623047538545, 0.756815440424, -0.197590874913), (0.735867145645, 0.481506196761, -0.476079117838), (-0.265162796549, -0.44202055565, -0.85691686861)-54.7118613403, 26.1063223936, -3.84815274522
3given(0.508448411993, -0.86039760554, 0.0345857300609), (-0.860744011012, -0.508975054073, -0.00800886007134), (0.0244940778564, -0.0256973678312, -0.999369644044)51.9164697023, 89.8412944278, -31.4792842528
4given(-0.292321033664, -0.744502307537, 0.600220565584), (-0.428390087312, 0.663084167346, 0.613841445414), (-0.855003126527, -0.077689774668, -0.512770857735)59.3969555889, 29.8988383264, -60.6577753508
5given(0.821218658987, -0.5541000464, -0.136282987603), (-0.566916639621, -0.819429203041, -0.0845062419247), (-0.0648493473476, 0.146659196039, -0.987059087576)36.8955349632, 116.977224051, -47.91821337

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Components

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


Mass: 46400.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SER33, YIL074C / Production host: Escherichia coli (E. coli)
References: UniProt: P40510, phosphoglycerate dehydrogenase, 2-oxoglutarate reductase
#2: Protein/peptide Poli-ALA


Mass: 698.854 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO4P / Feature type: SUBJECT OF INVESTIGATION
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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Porassium sodium tartrate tetrahydrate, 20%w/v PEG3350 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: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.19→47.78 Å / Num. obs: 40049 / % possible obs: 99.78 % / Redundancy: 6.6 % / Biso Wilson estimate: 126.1 Å2 / CC1/2: 1 / Net I/σ(I): 25.22
Reflection shellResolution: 3.19→3.304 Å / Num. unique obs: 3922 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YBA

1yba


Resolution: 3.19→47.78 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / Phase error: 33.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 3647 4.94 %
Rwork0.2294 --
obs0.2321 40035 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11604 0 196 0 11800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112008
X-RAY DIFFRACTIONf_angle_d1.26616516
X-RAY DIFFRACTIONf_dihedral_angle_d5.6081921
X-RAY DIFFRACTIONf_chiral_restr0.0682055
X-RAY DIFFRACTIONf_plane_restr0.012224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.230.46091190.3522346X-RAY DIFFRACTION84
3.23-3.280.3831420.34862731X-RAY DIFFRACTION98
3.28-3.320.33781450.32542698X-RAY DIFFRACTION98
3.32-3.370.39961400.33442720X-RAY DIFFRACTION97
3.37-3.420.44761400.3342605X-RAY DIFFRACTION94
3.42-3.480.38171390.32562698X-RAY DIFFRACTION98
3.48-3.540.33441460.31482767X-RAY DIFFRACTION99
3.54-3.60.35261440.30012728X-RAY DIFFRACTION99
3.6-3.670.33641450.29792747X-RAY DIFFRACTION99
3.67-3.750.31721450.29012749X-RAY DIFFRACTION98
3.75-3.830.37481420.28292692X-RAY DIFFRACTION98
3.83-3.920.39391380.28352694X-RAY DIFFRACTION96
3.92-4.020.28641390.26982712X-RAY DIFFRACTION97
4.02-4.130.30751390.262729X-RAY DIFFRACTION98
4.13-4.250.31551360.2352664X-RAY DIFFRACTION95
4.25-4.380.27111440.22292679X-RAY DIFFRACTION98
4.38-4.540.23691370.20472745X-RAY DIFFRACTION99
4.54-4.720.25261440.20052734X-RAY DIFFRACTION98
4.72-4.940.26541420.20842741X-RAY DIFFRACTION98
4.94-5.20.26881430.20182653X-RAY DIFFRACTION96
5.2-5.520.25681460.23412733X-RAY DIFFRACTION98
5.52-5.950.361430.24652689X-RAY DIFFRACTION97
5.95-6.550.28711350.24492764X-RAY DIFFRACTION98
6.55-7.490.24561380.22992709X-RAY DIFFRACTION97
7.49-9.420.22091390.17042687X-RAY DIFFRACTION97
9.42-47.780.24691370.182704X-RAY DIFFRACTION97

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