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

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Basic information

Entry
Database: PDB / ID: 8itc
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: 1.88 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)61,0816
Polymers59,8342
Non-polymers1,2474
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-8 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.388, 83.902, 103.828
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-QA0 / 5-(4-chlorophenyl)-3-[(4-phenylphenyl)sulfonylamino]phthalic acid


Mass: 507.942 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H18ClNO6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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 Å3/Da / Density % sol: 58.98 %
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: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 59389 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.084 / Χ2: 0.717 / Net I/σ(I): 4.9 / Num. measured all: 782738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.88-1.9513.60.958540.8820.9680.2520.9350.452100
1.95-2.0313.50.61658500.9360.9830.1740.6410.483100
2.03-2.1213.10.40858790.9690.9920.1160.4250.542100
2.12-2.2312.30.28858970.9790.9950.0840.30.606100
2.23-2.3713.70.2158760.9890.9970.0580.2190.693100
2.37-2.5513.60.15959070.9920.9980.0440.1650.774100
2.55-2.8112.70.11959280.9940.9990.0340.1240.81699.9
2.81-3.2113.60.08959320.9970.9990.0250.0920.992100
3.21-4.05130.06660350.99810.0190.0681.021100
4.05-5012.60.04862310.99910.0140.050.78599.6

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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: 1.88→26.7 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 2836 4.79 %
Rwork0.1934 --
obs0.1947 59160 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 83 381 4246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083975
X-RAY DIFFRACTIONf_angle_d0.985402
X-RAY DIFFRACTIONf_dihedral_angle_d13.413539
X-RAY DIFFRACTIONf_chiral_restr0.058558
X-RAY DIFFRACTIONf_plane_restr0.014700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.910.26921370.23642786X-RAY DIFFRACTION100
1.91-1.950.261540.23982765X-RAY DIFFRACTION100
1.95-1.980.29691230.24532765X-RAY DIFFRACTION100
1.98-2.030.30691370.23612791X-RAY DIFFRACTION100
2.03-2.070.26531380.22082779X-RAY DIFFRACTION100
2.07-2.120.19511350.20472811X-RAY DIFFRACTION100
2.12-2.170.24651360.21372803X-RAY DIFFRACTION100
2.17-2.230.24841440.20872787X-RAY DIFFRACTION100
2.23-2.290.23071400.20862788X-RAY DIFFRACTION100
2.29-2.370.22941490.21052774X-RAY DIFFRACTION100
2.37-2.450.24551260.2072829X-RAY DIFFRACTION100
2.45-2.550.22581140.20132806X-RAY DIFFRACTION100
2.55-2.670.24661570.20642814X-RAY DIFFRACTION100
2.67-2.810.22871410.19812812X-RAY DIFFRACTION100
2.81-2.980.2661560.20312798X-RAY DIFFRACTION100
2.98-3.210.20651270.19782828X-RAY DIFFRACTION100
3.21-3.540.21881790.19592812X-RAY DIFFRACTION100
3.54-4.050.21081440.17162869X-RAY DIFFRACTION100
4.05-5.090.1691270.15562908X-RAY DIFFRACTION100
5.09-26.70.2141720.20172999X-RAY DIFFRACTION100

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