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- PDB-5y2u: X-ray structure of Phosphoglycerate Mutase 1(PGAM1) complexed wit... -

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Basic information

Entry
Database: PDB / ID: 5y2u
TitleX-ray structure of Phosphoglycerate Mutase 1(PGAM1) complexed with a small molecule
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE/INHIBITOR / Phosphoglycerate Mutase 1 / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALIZARIN RED / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsJiang, L.L. / Zhou, L.
CitationJournal: To Be Published
Title: X-ray structure of Phosphoglycerate Mutase 1(PGAM1) complexed with a small molecule
Authors: Zhou, L. / Jiang, L.L.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Phosphoglycerate mutase 1
C: Phosphoglycerate mutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7056
Polymers59,8342
Non-polymers8714
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-8 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.640, 85.267, 102.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and segid B
21chain C and segid C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and segid BB0
211chain C and segid CC0

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Components

#1: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 29917.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1, PGAMA, CDABP0006 / Production host: Escherichia coli (E. coli)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AZN / ALIZARIN RED


Mass: 320.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8O7S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.02 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 8% PEG3350 100mM MES 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 47430 / % possible obs: 92.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 35.06 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.062 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.98-2.056.80.77846061.088190.8
2.05-2.136.80.56545541.08189.7
2.13-2.236.90.38545121.08189.4
2.23-2.356.80.28945781.085189.6
2.35-2.496.80.1945741.072189.7
2.49-2.696.90.14146241.049190.7
2.69-2.966.80.09847731.051193
2.96-3.396.50.06949911.008197
3.39-4.266.50.05750071.022196.1
4.26-5070.04652111.084196

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GPI

4gpi


Resolution: 1.98→43.544 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.96
RfactorNum. reflection% reflection
Rfree0.226 2401 5.07 %
Rwork0.1997 --
obs0.2011 47382 92.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.03 Å2 / Biso mean: 38.51 Å2 / Biso min: 22.26 Å2
Refinement stepCycle: final / Resolution: 1.98→43.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 57 209 4055
Biso mean--63.83 39.28 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083947
X-RAY DIFFRACTIONf_angle_d1.1575367
X-RAY DIFFRACTIONf_chiral_restr0.05561
X-RAY DIFFRACTIONf_plane_restr0.007689
X-RAY DIFFRACTIONf_dihedral_angle_d13.8231472
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2205X-RAY DIFFRACTION6.991TORSIONAL
12C2205X-RAY DIFFRACTION6.991TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9749-2.01520.28791420.25382448259087
2.0152-2.05910.25731380.24772567270591
2.0591-2.1070.29941400.24042526266690
2.107-2.15960.28251470.22232565271290
2.1596-2.2180.24971390.2262524266389
2.218-2.28330.2671320.23542549268189
2.2833-2.3570.26451380.21442523266189
2.357-2.44120.26811220.21242582270490
2.4412-2.5390.25411370.20672579271691
2.539-2.65450.23151510.21782592274390
2.6545-2.79440.23831310.20692644277592
2.7944-2.96950.25051410.22472709285094
2.9695-3.19870.26461420.21792775291796
3.1987-3.52040.25951560.21862811296798
3.5204-4.02950.21821370.18232826296396
4.0295-5.07560.16251300.15832797292794
5.0756-43.55450.18641780.18522964314297

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