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- PDB-5zrm: Phosphoglycerate mutase 1 complexed with a small molecule inhibit... -

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Basic information

Entry
Database: PDB / ID: 5zrm
TitlePhosphoglycerate mutase 1 complexed with a small molecule inhibitor In-AC
Components(Phosphoglycerate mutase ...) x 2
KeywordsISOMERASE/INHIBITOR / Phosphoglycerate mutase 1 / 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 / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9HU / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsJiang, L.L. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21472026 China
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 complexed with a small molecule inhibitor In-AC
Authors: Jiang, L.L. / Zhou, L.
History
DepositionApr 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: 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)54,1285
Polymers53,4442
Non-polymers6843
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-10 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.421, 82.971, 103.841
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Phosphoglycerate mutase ... , 2 types, 2 molecules BC

#1: Protein Phosphoglycerate mutase 1


Mass: 26682.377 Da / Num. of mol.: 1 / Fragment: UNP residues 2-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase
#2: Protein Phosphoglycerate mutase 1


Mass: 26761.350 Da / Num. of mol.: 1 / Fragment: UNP residues 2-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase

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Non-polymers , 4 types, 123 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: 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
#5: Chemical ChemComp-9HU / 2-[(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)sulfamoyl]phenyl acetate / 2-(N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)sulfamoyl)phenyl acetate


Mass: 453.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H15NO8S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: MES, pH 6.0, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 33372 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 47.21 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Χ2: 0.537 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.28-2.3660.62532960.8780.2740.6840.45999.5
2.36-2.466.20.47932670.9080.2070.5220.45599.6
2.46-2.576.20.35932900.9480.1540.3920.47799.7
2.57-2.76.80.27732890.9660.1140.30.49199.8
2.7-2.876.70.18733070.9830.0770.2020.52399.6
2.87-3.096.60.12933230.9920.0540.140.5699.9
3.09-3.416.30.08833190.9950.0370.0960.63899.9
3.41-3.96.90.06333520.9970.0260.0680.711100
3.9-4.916.30.04533940.9980.0190.0490.64899.7
4.91-506.40.03135350.9990.0130.0340.38799.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→37.056 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.78
RfactorNum. reflection% reflection
Rfree0.2324 1672 5.06 %
Rwork0.1955 --
obs0.1974 33047 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.44 Å2 / Biso mean: 50.61 Å2 / Biso min: 29.74 Å2
Refinement stepCycle: final / Resolution: 2.28→37.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 60 120 3941
Biso mean--80.49 47.57 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083906
X-RAY DIFFRACTIONf_angle_d1.015308
X-RAY DIFFRACTIONf_chiral_restr0.068553
X-RAY DIFFRACTIONf_plane_restr0.004683
X-RAY DIFFRACTIONf_dihedral_angle_d15.1071471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.34710.28911630.2482531269499
2.3471-2.42280.30181290.233725782707100
2.4228-2.50940.31531310.224125972728100
2.5094-2.60980.26741410.226725702711100
2.6098-2.72860.27671420.22325742716100
2.7286-2.87240.3311170.218126212738100
2.8724-3.05230.23991060.226326292735100
3.0523-3.28780.25981530.221325852738100
3.2878-3.61840.27181350.204526382773100
3.6184-4.14140.21181470.167626492796100
4.1414-5.21540.1671470.157126432790100
5.2154-37.0610.21411610.19572760292199

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