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- PDB-22wm: Phosphoglycerate mutase 1 complexed with a fragment -

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Basic information

Entry
Database: PDB / ID: 22wm
TitlePhosphoglycerate mutase 1 complexed with a fragment
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE / PGAM1 / Inhibitor
Function / homology
Function and homology information


bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / 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 / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily
Similarity search - Domain/homology
: / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsLi, S. / Zhou, L.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 complexed with a fragment
Authors: Li, S. / Zhou, L.
History
DepositionJan 26, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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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)61,45116
Polymers59,8342
Non-polymers1,61714
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-13 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.799, 83.959, 103.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BC

#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

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Non-polymers , 5 types, 181 molecules

#2: Chemical ChemComp-A1E4R / 4-(4-chlorophenyl)benzoic acid


Mass: 232.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9ClO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1 mM MES 6.0, 8% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 55088 / % possible obs: 97.6 % / Redundancy: 10.62 % / CC1/2: 0.9985 / CC star: 0.9996 / Rmerge(I) obs: 0.0583 / Rpim(I) all: 0.0182 / Rrim(I) all: 0.0612 / Net I/σ(I): 41.51
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 6.59 % / Rmerge(I) obs: 0.9732 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 3248 / CC1/2: 0.4527 / CC star: 0.7894 / Rpim(I) all: 0.4107 / Rrim(I) all: 1.062 / % possible all: 79.8

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Processing

Software
NameVersionClassification
PHENIX("2.0_5936": ???)refinement
autoPXdata processing
autoPXdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→23.19 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2756 5.01 %
Rwork0.1965 --
obs0.1982 54970 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→23.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 105 167 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084042
X-RAY DIFFRACTIONf_angle_d0.9085467
X-RAY DIFFRACTIONf_dihedral_angle_d18.2331525
X-RAY DIFFRACTIONf_chiral_restr0.052569
X-RAY DIFFRACTIONf_plane_restr0.01704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.940.3858980.31042033X-RAY DIFFRACTION77
1.94-1.980.35261120.28732230X-RAY DIFFRACTION84
1.98-2.020.30141270.25612439X-RAY DIFFRACTION91
2.02-2.060.27681330.24482621X-RAY DIFFRACTION99
2.06-2.10.26771490.23442646X-RAY DIFFRACTION100
2.1-2.150.28611330.22792647X-RAY DIFFRACTION100
2.15-2.210.24051460.22852643X-RAY DIFFRACTION100
2.21-2.270.27961580.2172628X-RAY DIFFRACTION100
2.27-2.330.21151330.21022641X-RAY DIFFRACTION100
2.33-2.410.2381230.21232698X-RAY DIFFRACTION100
2.41-2.490.27141710.2172604X-RAY DIFFRACTION100
2.49-2.590.26441280.22092679X-RAY DIFFRACTION100
2.59-2.710.2571210.21752682X-RAY DIFFRACTION100
2.71-2.850.24741150.21692700X-RAY DIFFRACTION100
2.85-3.030.23521490.22882673X-RAY DIFFRACTION100
3.03-3.270.24211280.21772696X-RAY DIFFRACTION100
3.27-3.590.22641650.20522680X-RAY DIFFRACTION100
3.59-4.110.21441480.17132705X-RAY DIFFRACTION100
4.11-5.170.17991520.15272755X-RAY DIFFRACTION100
5.17-23.190.20841670.172814X-RAY DIFFRACTION99

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