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- PDB-5kgm: 2.95A resolution structure of Apo independent phosphoglycerate mu... -

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Basic information

Entry
Database: PDB / ID: 5kgm
Title2.95A resolution structure of Apo independent phosphoglycerate mutase from C. elegans (monoclinic 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) / phosphoglycerate mutase activity / glucose catabolic process / glycolytic process / manganese ion binding / carbohydrate metabolic process / cytoplasm
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: 2.95 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 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)122,02910
Polymers121,6462
Non-polymers3838
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-61 kcal/mol
Surface area38070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.850, 94.375, 102.201
Angle α, β, γ (deg.)90.000, 96.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / 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

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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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 5000 MME, 0.1 M MES , 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: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→46.48 Å / Num. obs: 27020 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.55 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.09 / Rrim(I) all: 0.168 / Net I/σ(I): 9 / Num. measured all: 90718 / Scaling rejects: 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.95-3.133.50.625199.9
8.85-46.483.50.036198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.14data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O98

1o98


Resolution: 2.95→42.982 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 25.69
RfactorNum. reflection% reflection
Rfree0.2374 1353 5.01 %
Rwork0.184 --
obs0.1868 26993 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.94 Å2 / Biso mean: 48.5937 Å2 / Biso min: 18.54 Å2
Refinement stepCycle: final / Resolution: 2.95→42.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7837 0 8 0 7845
Biso mean--45.16 --
Num. residues----1037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088027
X-RAY DIFFRACTIONf_angle_d1.01310883
X-RAY DIFFRACTIONf_chiral_restr0.0591200
X-RAY DIFFRACTIONf_plane_restr0.0081440
X-RAY DIFFRACTIONf_dihedral_angle_d11.9844739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9501-3.05550.32611260.241825542680100
3.0555-3.17780.33831190.23125372656100
3.1778-3.32240.2791290.236325802709100
3.3224-3.49750.27261520.220925222674100
3.4975-3.71650.27851350.19892550268599
3.7165-4.00320.23611390.18192566270599
4.0032-4.40570.20671300.157725542684100
4.4057-5.04240.18841300.138625772707100
5.0424-6.34960.20751630.174625652728100
6.3496-42.98620.2151300.17172635276599

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