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- PDB-8it5: Phosphoglycerate mutase 1 complexed with a compound -

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Basic information

Entry
Database: PDB / ID: 8it5
TitlePhosphoglycerate mutase 1 complexed with a compound
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE/INHIBITOR / ISOMERASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


phosphoglycerate mutase activity / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...phosphoglycerate mutase activity / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-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
: / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, L. / Jiang, L.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 compound
Authors: Zhou, L. / Jiang, L.L.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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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)60,5355
Polymers59,8342
Non-polymers7013
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-11 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.377, 85.362, 102.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical ChemComp-QAI / 5-(4-chlorophenyl)-3-[(4-phenylphenyl)sulfonylamino]thiophene-2-carboxylic acid


Mass: 469.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16ClNO4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 59.19 %
Crystal growTemperature: 289 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: May 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37813 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.043 / Rrim(I) all: 0.155 / Χ2: 1.187 / Net I/σ(I): 3.9 / Num. measured all: 492979
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.28130.89837120.8510.9590.2580.9350.468100
2.28-2.3712.80.67337260.9030.9740.1950.7010.509100
2.37-2.4813.80.51337240.9380.9840.1430.5330.572100
2.48-2.6113.60.40337260.9550.9880.1130.4180.644100
2.61-2.7713.10.30137730.970.9920.0860.3140.791100
2.77-2.99130.23437180.9780.9940.0670.2441.01499.9
2.99-3.2913.60.18337880.9880.9970.0510.191.336100
3.29-3.7612.60.14837960.9910.9980.0440.1551.828100
3.76-4.7413.30.12338370.9930.9980.0350.1282.378100
4.74-5011.90.1140130.9940.9990.0340.1152.358100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data scaling
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.89 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1821 4.88 %
Rwork0.1888 --
obs0.1908 37353 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→26.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 44 187 4013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083933
X-RAY DIFFRACTIONf_angle_d0.9035341
X-RAY DIFFRACTIONf_dihedral_angle_d11.673532
X-RAY DIFFRACTIONf_chiral_restr0.05558
X-RAY DIFFRACTIONf_plane_restr0.01693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.25171390.21812692X-RAY DIFFRACTION100
2.26-2.330.26451520.20732672X-RAY DIFFRACTION100
2.33-2.40.25371360.20542692X-RAY DIFFRACTION100
2.4-2.490.24021380.20442710X-RAY DIFFRACTION100
2.49-2.590.25591200.2172732X-RAY DIFFRACTION100
2.59-2.70.27941370.21682701X-RAY DIFFRACTION100
2.7-2.850.29871570.20942712X-RAY DIFFRACTION100
2.85-3.020.27611440.22232689X-RAY DIFFRACTION100
3.02-3.260.23951560.22032718X-RAY DIFFRACTION100
3.26-3.580.27371380.20712750X-RAY DIFFRACTION100
3.58-4.10.21291560.1722743X-RAY DIFFRACTION100
4.1-5.160.17371230.15492812X-RAY DIFFRACTION100
5.16-26.890.19661250.17752909X-RAY DIFFRACTION99

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