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- PDB-8it6: Phosphoglycerate mutase 1 complexed with a compound -

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Basic information

Entry
Database: PDB / ID: 8it6
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: 2.55 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)60,4084
Polymers59,8342
Non-polymers5732
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-16 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.545, 88.584, 95.680
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-Q90 / 4-[4-chloranyl-2-(2-hydroxy-2-oxoethyloxy)phenyl]-2-[(4-phenylphenyl)sulfonylamino]benzoic acid


Mass: 537.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting 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: Jul 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 23615 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.047 / Rrim(I) all: 0.156 / Χ2: 0.588 / Net I/σ(I): 3.7 / Num. measured all: 254110
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.55-2.6411.30.83823190.8870.970.2580.8770.464100
2.64-2.7511.20.60223300.9370.9830.1870.6310.492100
2.75-2.8711.10.47223100.950.9870.1470.4940.505100
2.87-3.0210.90.35623370.9690.9920.1110.3730.53100
3.02-3.2110.20.24923280.9820.9950.0810.2620.5699.7
3.21-3.4610.80.19123460.990.9970.060.20.60799.9
3.46-3.8111.20.19523480.9880.9970.060.2040.972100
3.81-4.3610.80.09423840.9960.9990.030.0990.68599.9
4.36-5.4910.20.07223920.9970.9990.0240.0760.58999.9
5.49-509.90.05825210.99810.0190.0610.46799.6

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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: 2.55→30.01 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1153 4.9 %
Rwork0.1927 --
obs0.1962 23514 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 38 141 3961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083927
X-RAY DIFFRACTIONf_angle_d1.0475333
X-RAY DIFFRACTIONf_dihedral_angle_d8.384526
X-RAY DIFFRACTIONf_chiral_restr0.048558
X-RAY DIFFRACTIONf_plane_restr0.009694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.660.30461410.22322708X-RAY DIFFRACTION98
2.66-2.80.30381300.21162774X-RAY DIFFRACTION100
2.8-2.980.28131730.22212741X-RAY DIFFRACTION100
2.98-3.210.3371670.22232732X-RAY DIFFRACTION100
3.21-3.530.30031590.21682772X-RAY DIFFRACTION100
3.53-4.040.26791340.19612829X-RAY DIFFRACTION100
4.04-5.080.2081350.15312838X-RAY DIFFRACTION100
5.08-30.010.22571140.18132967X-RAY DIFFRACTION99

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