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- PDB-8pio: Crystal structure of Ser33 in complex with PHP (3-phosphohydroxyp... -

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Basic information

Entry
Database: PDB / ID: 8pio
TitleCrystal structure of Ser33 in complex with PHP (3-phosphohydroxypyruvate)
Componentsphosphoglycerate dehydrogenase
KeywordsCYTOSOLIC PROTEIN / Yeast protein
Function / homology2-oxo-3-(phosphonooxy)propanoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 PHP (3-phosphohydroxypyruvate)
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
F: phosphoglycerate dehydrogenase
A: phosphoglycerate dehydrogenase
B: phosphoglycerate dehydrogenase
C: phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,73016
Polymers204,9724
Non-polymers3,75812
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26350 Å2
ΔGint-136 kcal/mol
Surface area66220 Å2
Unit cell
Length a, b, c (Å)60.600, 95.150, 108.370
Angle α, β, γ (deg.)69.84, 88.72, 85.65
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21A
12F
22B
13F
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATYRTYRFA25 - 46925 - 469
21ALAALATYRTYRAB25 - 46925 - 469
12LEULEULEULEUFA38 - 46838 - 468
22GLYGLYLEULEUBC24 - 46824 - 468
13PROPROLEULEUFA39 - 46839 - 468
23PROPROLEULEUCD23 - 46823 - 468
14GLYGLYLEULEUAB24 - 46824 - 468
24GLYGLYLEULEUBC24 - 46824 - 468
15PROPROLEULEUAB23 - 46823 - 468
25PROPROLEULEUCD23 - 46823 - 468
16GLYGLYTYRTYRBC24 - 46924 - 469
26GLYGLYTYRTYRCD24 - 46924 - 469

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
phosphoglycerate dehydrogenase


Mass: 51243.039 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-HPV / 2-oxo-3-(phosphonooxy)propanoic acid / Hydroxypyruvic acid phosphate


Mass: 184.041 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG pH=6 25 % w/v PEG 1500 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: Feb 2, 2021
RadiationMonochromator: 0.9999 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.6→52.04 Å / Num. obs: 68361 / % possible obs: 97.87 % / Redundancy: 5.1 % / CC1/2: 0.992 / Net I/σ(I): 9.82
Reflection shellResolution: 2.6→2.693 Å / Mean I/σ(I) obs: 1.09 / Num. unique obs: 6350 / CC1/2: 0.604

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YBA

1yba


Resolution: 2.6→52.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 17.386 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 3369 4.9 %RANDOM
Rwork0.22237 ---
obs0.22431 64884 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.671 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å26.11 Å2-1.3 Å2
2--1.77 Å21.68 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.6→52.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12946 0 244 35 13225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313410
X-RAY DIFFRACTIONr_bond_other_d0.0040.01712241
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.63218287
X-RAY DIFFRACTIONr_angle_other_deg1.1511.57928317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15151739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51823.696560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.786152111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9871551
X-RAY DIFFRACTIONr_chiral_restr0.0350.21912
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022520
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6627.7916983
X-RAY DIFFRACTIONr_mcbond_other5.6637.7916982
X-RAY DIFFRACTIONr_mcangle_it8.38711.6848713
X-RAY DIFFRACTIONr_mcangle_other8.38611.6848714
X-RAY DIFFRACTIONr_scbond_it5.5488.0216427
X-RAY DIFFRACTIONr_scbond_other5.5458.026426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3411.9099575
X-RAY DIFFRACTIONr_long_range_B_refined10.99692.27214032
X-RAY DIFFRACTIONr_long_range_B_other10.99592.27814033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11F129500.06
12A129500.06
21F126010.06
22B126010.06
31F124890.05
32C124890.05
41A126630.05
42B126630.05
51A125610.05
52C125610.05
61B124960.05
62C124960.05
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 191 -
Rwork0.446 4284 -
obs--87.01 %

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