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- PDB-4o3f: Crystal Structure of mouse PGK1 3PG and terazosin(TZN) ternary complex -

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Basic information

Entry
Database: PDB / ID: 4o3f
TitleCrystal Structure of mouse PGK1 3PG and terazosin(TZN) ternary complex
ComponentsPhosphoglycerate kinase 1
KeywordsTRANSFERASE/TRANSFERASE ACTIVATOR / ENZYME-DRUG COMPLEX / TRANSFERASE-TRANSFERASE ACTIVATOR complex
Function / homology
Function and homology information


Glycolysis / Gluconeogenesis / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / positive regulation of oxidative phosphorylation / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis ...Glycolysis / Gluconeogenesis / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / positive regulation of oxidative phosphorylation / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / carbohydrate metabolic process / membrane raft / phosphorylation / extracellular space / ATP binding / cytoplasm / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / Chem-TZN / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.106 Å
AuthorsLi, X.L. / Finci, I.L. / Wang, J.H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Terazosin activates Pgk1 and Hsp90 to promote stress resistance.
Authors: Chen, X. / Zhao, C. / Li, X. / Wang, T. / Li, Y. / Cao, C. / Ding, Y. / Dong, M. / Finci, L. / Wang, J.H. / Li, X. / Liu, L.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1813
Polymers44,6071
Non-polymers5732
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.152, 71.397, 92.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

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Components

#1: Protein Phosphoglycerate kinase 1


Mass: 44607.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pgk1, Pgk-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09411, phosphoglycerate kinase
#2: Chemical ChemComp-TZN / [4-(4-amino-6,7-dimethoxyquinazolin-2-yl)piperazin-1-yl][(2R)-tetrahydrofuran-2-yl]methanone / Terazosin


Mass: 387.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N5O4 / Comment: medication*YM
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25-30% PEG 4000,0.1 M Tris-HCl pH 8.0, 0.2 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 8, 2013
RadiationMonochromator: NUMERICAL LINK TYPE DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 25250 / Num. obs: 23106 / % possible obs: 91.5 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.1-2.141100
2.14-2.181100
2.18-2.221100
2.22-2.261100
2.26-2.311100
2.31-2.371100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C39

3c39


Resolution: 2.106→49.796 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 2000 8.66 %
Rwork0.1823 --
obs0.185 23100 99.39 %
all-23100 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.106→49.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 39 232 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153141
X-RAY DIFFRACTIONf_angle_d1.2814234
X-RAY DIFFRACTIONf_dihedral_angle_d14.7771182
X-RAY DIFFRACTIONf_chiral_restr0.086482
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1064-2.15910.29961310.23831381X-RAY DIFFRACTION93
2.1591-2.21750.33171390.23381463X-RAY DIFFRACTION100
2.2175-2.28270.27821420.23251497X-RAY DIFFRACTION100
2.2827-2.35640.29281410.22261486X-RAY DIFFRACTION100
2.3564-2.44060.30261430.2171510X-RAY DIFFRACTION100
2.4406-2.53830.28661400.23561485X-RAY DIFFRACTION100
2.5383-2.65380.29611440.22571517X-RAY DIFFRACTION100
2.6538-2.79370.27411420.22551491X-RAY DIFFRACTION100
2.7937-2.96870.25241440.22561526X-RAY DIFFRACTION100
2.9687-3.19790.26571430.19611511X-RAY DIFFRACTION100
3.1979-3.51970.2121440.18451515X-RAY DIFFRACTION100
3.5197-4.02880.15941450.15641537X-RAY DIFFRACTION100
4.0288-5.07510.15281480.13891551X-RAY DIFFRACTION100
5.0751-49.80940.16441540.15311630X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.2873 Å / Origin y: -17.0575 Å / Origin z: -24.2834 Å
111213212223313233
T0.2278 Å2-0.0039 Å20.0251 Å2-0.205 Å20.0219 Å2--0.2096 Å2
L1.0318 °20.1581 °20.4791 °2-0.2535 °20.073 °2--0.5588 °2
S0.0433 Å °-0.0841 Å °-0.0977 Å °0.0097 Å °-0.0541 Å °-0.0237 Å °0.1188 Å °-0.0218 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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