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- PDB-7tl8: 1.95A resolution structure of independent phosphoglycerate mutase... -

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Basic information

Entry
Database: PDB / ID: 7tl8
Title1.95A resolution structure of independent phosphoglycerate mutase from S. aureus in complex with a macrocyclic peptide inhibitor (Sa-D3)
Components
  • 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
  • Peptide Sa-D3
KeywordsISOMERASE/Inhibitor / phosphoglycerate mutase / ipglycermide / macrocyclic peptide inhibitors / metal ion binding / ISOMERASE / ISOMERASE-Inhibitor complex
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 / cytoplasm
Similarity search - Function
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-like, core domain superfamily
Similarity search - Domain/homology
: / : / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLiu, L. / Lovell, S. / Battaile, K.P. / Dranchak, P. / Queme, B. / Aitha, M. / van Neer, R.H.P. / Kimura, H. / Katho, T. / Suga, H. / Inglese, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases.
Authors: van Neer, R.H.P. / Dranchak, P.K. / Liu, L. / Aitha, M. / Queme, B. / Kimura, H. / Katoh, T. / Battaile, K.P. / Lovell, S. / Inglese, J. / Suga, H.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Peptide Sa-D3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2374
Polymers59,1272
Non-polymers1102
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-18 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.898, 74.172, 75.017
Angle α, β, γ (deg.)90.000, 100.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / BPG-independent PGAM / Phosphoglyceromutase / iPGM


Mass: 57316.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pgm_1, gpmI, pgm_2 / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W8U5L7, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
#2: Protein/peptide Peptide Sa-D3


Type: Cyclic peptide / Class: Inhibitor / Mass: 1809.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002492
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.17 Å3/Da / Density % sol: 43.3 % / Mosaicity: 0.19 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 100 mM Bis-Tris, 200 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→46.11 Å / Num. obs: 36494 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.3 / Num. measured all: 123194 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-23.50.816884525550.6051.699.5
8.94-46.113.40.02413634040.99935.597.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.20_4438refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MY4

4my4


Resolution: 1.95→46.11 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 1728 4.74 %
Rwork0.1943 34729 -
obs0.1971 36457 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.96 Å2 / Biso mean: 36.4182 Å2 / Biso min: 12.6 Å2
Refinement stepCycle: final / Resolution: 1.95→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3857 0 2 231 4090
Biso mean--20.27 36.45 -
Num. residues----503
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 (%)
1.95-2.010.3341400.27642862300299
2.01-2.070.28951290.24782928305799
2.07-2.150.33321270.23942894302199
2.15-2.230.27761520.23362857300998
2.23-2.330.271580.21932883304199
2.33-2.460.29891290.213829293058100
2.46-2.610.25981660.20112884305099
2.61-2.810.29141480.20342864301298
2.81-3.10.2271630.19962901306499
3.1-3.540.27371410.18912908304999
3.54-4.460.21261310.15942882301398
4.46-46.110.22321440.17282937308197

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