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- PDB-8pir: Crystal structure of Ser33 in complex with 3-PGA (3-phosphoglycerate) -

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Basic information

Entry
Database: PDB / ID: 8pir
TitleCrystal structure of Ser33 in complex with 3-PGA (3-phosphoglycerate)
Componentsphosphoglycerate dehydrogenase
KeywordsCYTOSOLIC PROTEIN / Enzyme Protein
Function / homology3-PHOSPHOGLYCERIC ACID / 1,4-BUTANEDIOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 with 3-PGA (3-phosphoglycerate)
Authors: Perrone, S. / Cifuente, J.O. / Marina, A. / Mastrella, L. / Trastoy, B. / Linster, C.L. / 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

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Assembly

Deposited unit
F: phosphoglycerate dehydrogenase
A: phosphoglycerate dehydrogenase
B: phosphoglycerate dehydrogenase
C: phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,82016
Polymers206,0614
Non-polymers3,75812
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28740 Å2
ΔGint-137 kcal/mol
Surface area66630 Å2
Unit cell
Length a, b, c (Å)60.599, 95.726, 109.252
Angle α, β, γ (deg.)69.92, 89.53, 86.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
phosphoglycerate dehydrogenase


Mass: 51515.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SER33 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4BZ61
#2: 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
#3: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol 0.1M Sodium HEPES; MOPS (acid) pH=7.5 20% v/v Glycerol; 10% w/v PEG 4000 ...Details: 0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol 0.1M Sodium HEPES; MOPS (acid) pH=7.5 20% v/v Glycerol; 10% w/v PEG 4000 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: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→60.45 Å / Num. obs: 61940 / % possible obs: 97.73 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 13.01
Reflection shellResolution: 2.7→2.797 Å / Mean I/σ(I) obs: 2.61 / Num. unique obs: 6232 / CC1/2: 0.905

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→60.45 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 3126 5.06 %
Rwork0.2155 --
obs0.217 61784 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→60.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13040 0 244 35 13319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313508
X-RAY DIFFRACTIONf_angle_d1.66218405
X-RAY DIFFRACTIONf_dihedral_angle_d14.2154812
X-RAY DIFFRACTIONf_chiral_restr0.0972220
X-RAY DIFFRACTIONf_plane_restr0.0132420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.36881410.34072710X-RAY DIFFRACTION98
2.74-2.790.33911520.3182639X-RAY DIFFRACTION98
2.79-2.840.32071380.29352664X-RAY DIFFRACTION98
2.84-2.890.34311540.28062726X-RAY DIFFRACTION98
2.89-2.940.33091550.27212601X-RAY DIFFRACTION98
2.94-30.29621360.27422696X-RAY DIFFRACTION98
3-3.070.32651480.27762679X-RAY DIFFRACTION98
3.07-3.140.31591510.27532645X-RAY DIFFRACTION98
3.14-3.220.31811400.27372704X-RAY DIFFRACTION98
3.22-3.30.30661370.2662673X-RAY DIFFRACTION97
3.3-3.40.30271320.24692675X-RAY DIFFRACTION99
3.4-3.510.31181300.24692604X-RAY DIFFRACTION95
3.51-3.640.27671510.24152689X-RAY DIFFRACTION99
3.64-3.780.29051200.2532664X-RAY DIFFRACTION96
3.78-3.950.25691370.25442528X-RAY DIFFRACTION95
3.95-4.160.21871260.20132711X-RAY DIFFRACTION98
4.16-4.420.24681370.18432674X-RAY DIFFRACTION98
4.42-4.770.1871380.17652705X-RAY DIFFRACTION98
4.77-5.240.20441500.17842661X-RAY DIFFRACTION98
5.24-60.21371700.20012668X-RAY DIFFRACTION98
6-7.560.20231660.19022663X-RAY DIFFRACTION98
7.56-60.450.17581170.15362679X-RAY DIFFRACTION98

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