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- PDB-7xb8: Phosphoglycerate mutase 1 complexed with a covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 7xb8
TitlePhosphoglycerate mutase 1 complexed with a covalent inhibitor
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE/INHIBITOR / ISOMERASE-INHIBITOR COMPLEX
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 / cytosol / cytoplasm
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
Chem-H6I / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJiang, L.L. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077019 China
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 complexed with a covalent inhibitor
Authors: Jiang, L.L. / Zhou, L.
History
DepositionMar 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)60,7175
Polymers59,8342
Non-polymers8823
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-16 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.380, 73.234, 168.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-H6I / 4-(cyclopenten-1-yl)-2-[(3-sulfophenyl)sulfonylamino]benzoic acid


Mass: 423.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17NO7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.8 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG3350, 100mM MES 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 65989 / % possible obs: 97.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Χ2: 0.975 / Net I/σ(I): 5.5 / Num. measured all: 807259
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6612.40.49562770.9530.140.5150.56694.6
1.66-1.7212.40.38963170.9720.1110.4050.62895.4
1.72-1.811.90.30863740.9770.090.3210.69795.7
1.8-1.911.90.24164620.9850.070.2510.78196.7
1.9-2.0212.20.19165610.990.0550.1990.95698.1
2.02-2.1711.70.1566340.9920.0450.1561.09498.9
2.17-2.3912.30.12266860.9930.0360.1281.21199.1
2.39-2.7412.50.10167560.9950.030.1061.21699.9
2.74-3.4512.80.07868110.9970.0220.0811.24199.7
3.45-5012.30.05971110.9980.0170.0621.24599.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GPI

4gpi


Resolution: 1.6→25.84 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 3195 4.88 %
Rwork0.1668 62241 -
obs0.1679 65436 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.19 Å2 / Biso mean: 19.7953 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 1.6→25.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 1 515 4472
Biso mean--10.59 28.71 -
Num. residues----486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.25091360.18962566270294
1.62-1.650.20081230.18162571269495
1.65-1.680.2211090.17442662277195
1.68-1.710.19651580.16912556271495
1.71-1.740.2181570.16282552270996
1.74-1.770.20431180.17052656277496
1.77-1.810.20971220.17452598272096
1.81-1.840.20911250.17662664278996
1.84-1.890.21221290.17172659278898
1.89-1.940.18881460.17792700284698
1.94-1.990.21811240.17242690281498
1.99-2.050.20871410.16822709285099
2.05-2.110.19871530.16642721287499
2.11-2.190.20521370.1682680281798
2.19-2.270.20231390.17142760289999
2.27-2.380.17991270.170127772904100
2.38-2.50.20781410.170827502891100
2.5-2.660.20571470.176227672914100
2.66-2.870.1781590.171627672926100
2.87-3.150.19921310.170327902921100
3.15-3.610.18751510.163228282979100
3.61-4.540.16791750.138728283003100
4.54-25.840.15971470.170129903137100

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