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- PDB-8pis: Crystal structure of Ser33 in complex with L-Serine -

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Basic information

Entry
Database: PDB / ID: 8pis
TitleCrystal structure of Ser33 in complex with L-Serine
Components(phosphoglycerate dehydrogenase) x 2
KeywordsCYTOSOLIC PROTEIN / Enzyme protein
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / SERINE / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 L-Serine
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

Downloads & links

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Assembly

Deposited unit
A: phosphoglycerate dehydrogenase
B: phosphoglycerate dehydrogenase
C: phosphoglycerate dehydrogenase
D: phosphoglycerate dehydrogenase
E: phosphoglycerate dehydrogenase
F: phosphoglycerate dehydrogenase
G: phosphoglycerate dehydrogenase
H: phosphoglycerate dehydrogenase
I: phosphoglycerate dehydrogenase
J: phosphoglycerate dehydrogenase
K: phosphoglycerate dehydrogenase
M: phosphoglycerate dehydrogenase
N: phosphoglycerate dehydrogenase
O: phosphoglycerate dehydrogenase
Q: phosphoglycerate dehydrogenase
L: phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,22332
Polymers419,07516
Non-polymers6,14816
Water4,017223
1
A: phosphoglycerate dehydrogenase
B: phosphoglycerate dehydrogenase
C: phosphoglycerate dehydrogenase
D: phosphoglycerate dehydrogenase
J: phosphoglycerate dehydrogenase
K: phosphoglycerate dehydrogenase
M: phosphoglycerate dehydrogenase
O: phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,61116
Polymers209,5378
Non-polymers3,0748
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: phosphoglycerate dehydrogenase
F: phosphoglycerate dehydrogenase
G: phosphoglycerate dehydrogenase
H: phosphoglycerate dehydrogenase
I: phosphoglycerate dehydrogenase
N: phosphoglycerate dehydrogenase
Q: phosphoglycerate dehydrogenase
L: phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,61116
Polymers209,5378
Non-polymers3,0748
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.115, 110.735, 117.027
Angle α, β, γ (deg.)64.42, 65.95, 67.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
phosphoglycerate dehydrogenase


Mass: 51515.289 Da / Num. of mol.: 8
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: Protein/peptide
phosphoglycerate dehydrogenase


Mass: 869.063 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic 0.1 M Bis-Tris propane pH 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: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.69→43.11 Å / Num. obs: 114590 / % possible obs: 96.97 % / Redundancy: 4.3 % / CC1/2: 0.988 / CC star: 0.997 / Net I/σ(I): 9.57
Reflection shellResolution: 2.691→2.787 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 10826 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→43.11 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 5996 5.26 %
Rwork0.2157 --
obs0.2184 114028 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25922 0 0 223 26145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01326376
X-RAY DIFFRACTIONf_angle_d1.03136007
X-RAY DIFFRACTIONf_dihedral_angle_d10.8779152
X-RAY DIFFRACTIONf_chiral_restr0.0574374
X-RAY DIFFRACTIONf_plane_restr0.0064597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.720.37611310.29852943X-RAY DIFFRACTION78
2.72-2.750.38441840.26683608X-RAY DIFFRACTION96
2.75-2.790.30881830.23993665X-RAY DIFFRACTION97
2.79-2.820.30511570.24323550X-RAY DIFFRACTION96
2.82-2.860.31021710.23373588X-RAY DIFFRACTION96
2.86-2.90.33431930.23363584X-RAY DIFFRACTION97
2.9-2.940.29312010.24033626X-RAY DIFFRACTION97
2.94-2.980.32461780.24233669X-RAY DIFFRACTION98
2.98-3.030.32831880.2473620X-RAY DIFFRACTION98
3.03-3.080.31321910.2483629X-RAY DIFFRACTION98
3.08-3.130.28531990.24983624X-RAY DIFFRACTION98
3.13-3.190.32542090.24343627X-RAY DIFFRACTION98
3.19-3.250.27171830.23913661X-RAY DIFFRACTION97
3.25-3.320.321820.23123605X-RAY DIFFRACTION97
3.32-3.390.32752000.22553604X-RAY DIFFRACTION97
3.39-3.470.26862080.21823674X-RAY DIFFRACTION98
3.47-3.560.28812270.22183624X-RAY DIFFRACTION99
3.56-3.650.28152320.22683640X-RAY DIFFRACTION98
3.65-3.760.27162280.23333626X-RAY DIFFRACTION98
3.76-3.880.282250.22293603X-RAY DIFFRACTION98
3.88-4.020.25682400.20083641X-RAY DIFFRACTION98
4.02-4.180.24921950.19373658X-RAY DIFFRACTION99
4.18-4.370.23482030.18983678X-RAY DIFFRACTION99
4.37-4.60.23192540.18423603X-RAY DIFFRACTION99
4.6-4.890.21542350.19273630X-RAY DIFFRACTION98
4.89-5.260.24491880.20263674X-RAY DIFFRACTION99
5.26-5.790.26591980.21763659X-RAY DIFFRACTION98
5.79-6.630.26271640.21613695X-RAY DIFFRACTION99
6.63-8.340.2432000.19273666X-RAY DIFFRACTION99
8.34-43.110.18072490.18083358X-RAY DIFFRACTION92

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