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- PDB-8it7: Phosphoglycerate mutase 1 complexed with a compound -

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Basic information

Entry
Database: PDB / ID: 8it7
TitlePhosphoglycerate mutase 1 complexed with a compound
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 / 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: 2.8 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

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)60,5455
Polymers59,8342
Non-polymers7113
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-9 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.194, 85.593, 101.304
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-Q9F / 4-(4-chlorophenyl)-2-oxidanyl-6-[(4-phenylphenyl)sulfonylamino]benzoic acid


Mass: 479.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H18ClNO5S / Feature type: SUBJECT OF INVESTIGATION
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: 2.98 Å3/Da / Density % sol: 58.69 %
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: BL18U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17933 / % possible obs: 98.9 % / Redundancy: 12.9 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.068 / Rrim(I) all: 0.249 / Χ2: 0.513 / Net I/σ(I): 2.6 / Num. measured all: 231246
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.911.51.34917380.7630.930.411.4120.41198
2.9-3.0212.81.18117730.8580.9610.3391.230.42499.7
3.02-3.1513.30.9117860.9310.9820.2570.9460.43999.8
3.15-3.3213.40.7317690.9470.9860.2050.7580.44799.8
3.32-3.5313.30.5117570.970.9920.1440.5310.46998.4
3.53-3.812.50.31817690.9680.9920.0930.3320.51998.2
3.8-4.1813.90.20717930.9930.9980.0570.2150.57599.6
4.18-4.7913.40.14918240.9950.9990.0420.1540.64399.6
4.79-6.0312.70.13317960.9940.9990.0380.1390.59597.3
6.03-5012.30.08319280.9980.9990.0240.0860.5898.7

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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: 2.8→31.91 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 849 4.76 %
Rwork0.1922 --
obs0.1949 17841 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 46 0 3828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093935
X-RAY DIFFRACTIONf_angle_d1.0165344
X-RAY DIFFRACTIONf_dihedral_angle_d11.103532
X-RAY DIFFRACTIONf_chiral_restr0.049558
X-RAY DIFFRACTIONf_plane_restr0.009693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.31161450.24692733X-RAY DIFFRACTION97
2.98-3.210.29921440.22462814X-RAY DIFFRACTION100
3.21-3.530.28891380.222809X-RAY DIFFRACTION99
3.53-4.040.27781310.18712836X-RAY DIFFRACTION99
4.04-5.090.19811370.16722890X-RAY DIFFRACTION99
5.09-31.910.23081540.18312910X-RAY DIFFRACTION97

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