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- PDB-5kgl: 2.45A resolution structure of Apo independent phosphoglycerate mu... -

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Basic information

Entry
Database: PDB / ID: 5kgl
Title2.45A resolution structure of Apo independent phosphoglycerate mutase from C. elegans (orthorhombic form)
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE / metal binding / coupled enzyme assay / HTS / structure activity relationship / RaPID systems / high throughput enzymology
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glucose catabolic process / glycolytic process / manganese ion binding / carbohydrate metabolic process / cytosol
Similarity search - Function
2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain / BPG-independent phosphoglycerate mutase, domain B / Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent / BPG-independent PGAM, N-terminal / BPG-independent phosphoglycerate mutase, domain B superfamily / BPG-independent PGAM N-terminus (iPGM_N) / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A ...2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain / BPG-independent phosphoglycerate mutase, domain B / Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent / BPG-independent PGAM, N-terminal / BPG-independent phosphoglycerate mutase, domain B superfamily / BPG-independent PGAM N-terminus (iPGM_N) / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Yu, H. / Dranchak, P. / MacArthur, R. / Li, Z. / Carlow, T. / Suga, H. / Inglese, J.
CitationJournal: Nat Commun / Year: 2017
Title: Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases.
Authors: Yu, H. / Dranchak, P. / Li, Z. / MacArthur, R. / Munson, M.S. / Mehzabeen, N. / Baird, N.J. / Battalie, K.P. / Ross, D. / Lovell, S. / Carlow, C.K. / Suga, H. / Inglese, J.
History
DepositionJun 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,63015
Polymers121,6462
Non-polymers98413
Water4,216234
1
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2677
Polymers60,8231
Non-polymers4446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3638
Polymers60,8231
Non-polymers5407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.321, 98.852, 173.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that this particular crystal form was monomeric

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / iPGM / Cofactor-independent phosphoglycerate mutase homolog


Mass: 60823.000 Da / Num. of mol.: 2 / Fragment: isoform a
Source method: isolated from a genetically manipulated source
Details: Full length (M1 to I539, isoform a) / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ipgm-1, F57B10.3 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C2566/T7 Express
References: UniProt: G5EFZ1, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)

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Non-polymers , 5 types, 247 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→98.85 Å / Num. obs: 43707 / % possible obs: 97.5 % / Redundancy: 5 % / Biso Wilson estimate: 24.61 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.099 / Rrim(I) all: 0.229 / Net I/σ(I): 7.6 / Num. measured all: 217179 / Scaling rejects: 3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.45-2.544.70.84199.4
9.17-98.855.20.051190.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.11 Å40.44 Å
Translation4.11 Å40.44 Å

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IFY

2ify


Resolution: 2.45→40.437 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.2595 2137 4.89 %
Rwork0.1846 --
obs0.1883 43673 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.97 Å2 / Biso mean: 25.1509 Å2 / Biso min: 5.37 Å2
Refinement stepCycle: final / Resolution: 2.45→40.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7886 0 41 234 8161
Biso mean--41 20.91 -
Num. residues----1040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098106
X-RAY DIFFRACTIONf_angle_d0.93610992
X-RAY DIFFRACTIONf_chiral_restr0.051202
X-RAY DIFFRACTIONf_plane_restr0.0061452
X-RAY DIFFRACTIONf_dihedral_angle_d11.5264778
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.5070.34061590.24852801296099
2.507-2.56970.30261420.2372778292099
2.5697-2.63910.3221400.23132780292098
2.6391-2.71680.32471680.22052773294198
2.7168-2.80450.30361300.21082791292198
2.8045-2.90470.30071520.21252758291098
2.9047-3.02090.33521430.22652771291497
3.0209-3.15840.29251290.2192751288097
3.1584-3.32480.33521550.2172719287496
3.3248-3.5330.2391200.18242810293097
3.533-3.80560.23321420.15942753289597
3.8056-4.18820.20241450.13812777292296
4.1882-4.79340.17381330.12672754288795
4.7934-6.0360.20971270.15552751287893
6.036-40.44240.22811520.18062769292191

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