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- PDB-5y2i: Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PG... -

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Basic information

Entry
Database: PDB / ID: 5y2i
TitlePhosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PGMI-004A
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE/INHIBITOR / phosphoglycerate mutase / 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
Chem-8KX / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.917 Å
AuthorsJiang, L. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC21472026 China
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 (PGAM1) complexed with its inhibitor PGMI-004A
Authors: Jiang, L. / Zhou, L.
History
DepositionJul 26, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,5285
Polymers59,8342
Non-polymers6943
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-11 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.762, 85.036, 102.480
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
21chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASP / End label comp-ID: ASP

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain BBA3 - 2353 - 235
2chain CCB2 - 2352 - 235

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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-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase
#2: Chemical ChemComp-8KX / 3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)-~{N}-[4-(trifluoromethyl)phenyl]anthracene-2-sulfonamide


Mass: 463.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H12F3NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 280 / 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: 3.01 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97737 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97737 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55599 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 37.78 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Χ2: 1.456 / Net I/σ(I): 6.1 / Num. measured all: 716201
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.9-1.9713.10.89855070.8970.2540.9330.503
1.97-2.0512.90.62554510.9480.1790.6510.563
2.05-2.1412.20.45954880.960.1360.4790.662
2.14-2.25130.3255280.9820.0910.3320.823
2.25-2.3913.40.24855030.9870.0690.2581.025
2.39-2.5813.30.19955100.990.0560.2071.337
2.58-2.8412.40.15855410.9920.0470.1651.882
2.84-3.2513.60.1255910.9960.0340.1252.471
3.25-4.0912.40.09156160.9960.0270.0952.998
4.09-5012.60.06558640.9980.0190.0682.227

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIXphenix.refine: 1.8.2_1309refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GPI

4gpi


Resolution: 1.917→43.566 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.2136 2822 5.08 %
Rwork0.1907 --
obs0.1919 55518 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.42 Å2 / Biso mean: 35.28 Å2 / Biso min: 20.99 Å2
Refinement stepCycle: final / Resolution: 1.917→43.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 45 280 4082
Biso mean--53.47 37.71 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083902
X-RAY DIFFRACTIONf_angle_d1.1995302
X-RAY DIFFRACTIONf_chiral_restr0.051553
X-RAY DIFFRACTIONf_plane_restr0.007683
X-RAY DIFFRACTIONf_dihedral_angle_d13.9931473
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2228X-RAY DIFFRACTION7.798TORSIONAL
12C2228X-RAY DIFFRACTION7.798TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.917-1.95010.25121150.25262035215078
1.9501-1.98550.26991310.225226352766100
1.9855-2.02370.27231310.214126442775100
2.0237-2.0650.26451380.207326372775100
2.065-2.10990.2461280.2126292757100
2.1099-2.1590.25231700.198625992769100
2.159-2.2130.23111370.191526442781100
2.213-2.27280.20951380.180726542792100
2.2728-2.33970.19981520.179626292781100
2.3397-2.41520.21291370.183726572794100
2.4152-2.50150.22661270.195726532780100
2.5015-2.60170.24621570.196426182775100
2.6017-2.72010.19681480.194226632811100
2.7201-2.86350.24731370.202326792816100
2.8635-3.04280.25031410.207426632804100
3.0428-3.27770.24421400.198726772817100
3.2777-3.60740.22861460.211526862832100
3.6074-4.1290.17981520.170527022854100
4.129-5.20080.17031510.159627212872100
5.2008-43.57730.21351460.200428713017100

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