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- PDB-5zs8: Acetylation of lysine 100 of Phosphoglycerate mutase 1 complexed ... -

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Basic information

Entry
Database: PDB / ID: 5zs8
TitleAcetylation of lysine 100 of Phosphoglycerate mutase 1 complexed with KH_ol
Components(Phosphoglycerate mutase ...) x 2
KeywordsISOMERASE / Phosphoglycerate mutase 1
Function / homology
Function and homology information


bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 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 / 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-9JF / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsJiang, L.L. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21472026 China
CitationJournal: To Be Published
Title: Acetylation of lysine 100 of Phosphoglycerate mutase 1 complexed with KH_ol
Authors: Jiang, L.L. / Zhou, L.
History
DepositionApr 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 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)54,8725
Polymers54,2302
Non-polymers6423
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-8 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.743, 83.101, 100.368
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 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 26682.377 Da / Num. of mol.: 1
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: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 27547.215 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 240 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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-9JF / N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)-2-hydroxybenzene-1-sulfonamide


Mass: 411.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H13NO7S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: MES, pH 6.0, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34396 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 41.38 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Χ2: 0.899 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.40.80433840.7490.3440.8760.625100
2.28-2.376.30.54333750.8770.2350.5930.478100
2.37-2.485.90.38633930.9270.1720.4240.523100
2.48-2.616.20.30233970.9510.1310.330.53799.9
2.61-2.776.60.21534060.9740.090.2330.643100
2.77-2.996.50.15234190.9860.0640.1650.762100
2.99-3.296.10.10534370.9920.0460.1151.00599.9
3.29-3.766.60.07634440.9960.0320.0831.40599.9
3.76-4.746.20.05434860.9970.0240.0591.65999.8
4.74-506.10.04336550.9970.0190.0481.28999.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
HKL-2000data collection
PHASERphasing
RefinementResolution: 2.2→49.669 Å / FOM work R set: 0.8588 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 1720 5.05 %
Rwork0.1787 32333 -
obs0.1808 34053 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.57 Å2 / Biso mean: 40.53 Å2 / Biso min: 20.55 Å2
Refinement stepCycle: final / Resolution: 2.2→49.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 55 237 4108
Biso mean--73.44 42.23 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083965
X-RAY DIFFRACTIONf_angle_d1.0455388
X-RAY DIFFRACTIONf_chiral_restr0.073562
X-RAY DIFFRACTIONf_plane_restr0.005695
X-RAY DIFFRACTIONf_dihedral_angle_d14.8881496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.26480.26721280.22426222750
2.2648-2.33790.24581490.20326722821
2.3379-2.42140.24721440.190426332777
2.4214-2.51840.23041520.192526572809
2.5184-2.6330.25941310.185126792810
2.633-2.77180.23921480.179226812829
2.7718-2.94540.24281350.184826782813
2.9454-3.17280.21541570.184926912848
3.1728-3.4920.26141400.185126832823
3.492-3.99710.20541340.161127382872
3.9971-5.03520.17591560.152227262882
5.0352-49.68140.22091460.192728733019

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