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- PDB-7kng: 2.10A resolution structure of independent Phosphoglycerate mutase... -

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Basic information

Entry
Database: PDB / ID: 7kng
Title2.10A resolution structure of independent Phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Ce-2 Y7F)
Components
  • 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
  • DTY-ASP-TYR-PRO-GLY-ASP-PHE-CYS-TYR-LEU-TYR-GLY-THR-CYS
KeywordsISOMERASE / phosphoglycerate mutase / ipglycermide / peptide inhibitors / metal ion binding
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-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: 2.1 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Weidmann, M. / Dranchak, P. / Aitha, M. / Queme, B. / Collmus, C.D. / Kanter, L. / Lamy, L. ...Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Weidmann, M. / Dranchak, P. / Aitha, M. / Queme, B. / Collmus, C.D. / Kanter, L. / Lamy, L. / Tao, D. / Rai, G. / Suga, H. / Inglese, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)1ZIATR000247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structure-activity relationship of ipglycermide binding to phosphoglycerate mutases.
Authors: Wiedmann, M. / Dranchak, P.K. / Aitha, M. / Queme, B. / Collmus, C.D. / Kashipathy, M.M. / Kanter, L. / Lamy, L. / Rogers, J.M. / Tao, D. / Battaile, K.P. / Rai, G. / Lovell, S. / Suga, H. / Inglese, J.
History
DepositionNov 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: DTY-ASP-TYR-PRO-GLY-ASP-PHE-CYS-TYR-LEU-TYR-GLY-THR-CYS
D: DTY-ASP-TYR-PRO-GLY-ASP-PHE-CYS-TYR-LEU-TYR-GLY-THR-CYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,41716
Polymers121,9224
Non-polymers49512
Water7,188399
1
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
C: DTY-ASP-TYR-PRO-GLY-ASP-PHE-CYS-TYR-LEU-TYR-GLY-THR-CYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2098
Polymers60,9612
Non-polymers2486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-99 kcal/mol
Surface area19420 Å2
MethodPISA
2
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
D: DTY-ASP-TYR-PRO-GLY-ASP-PHE-CYS-TYR-LEU-TYR-GLY-THR-CYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2098
Polymers60,9612
Non-polymers2486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-100 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.862, 75.471, 101.360
Angle α, β, γ (deg.)90.000, 99.110, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 59257.102 Da / Num. of mol.: 2 / Fragment: M19 to I539 (isoform b)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ipgm-1, F57B10.3 / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G5EFZ1, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
#2: Protein/peptide DTY-ASP-TYR-PRO-GLY-ASP-PHE-CYS-TYR-LEU-TYR-GLY-THR-CYS


Mass: 1703.871 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Chains C and D are an N-terminal acetylated peptide with a D-Tyr at position 1. The acetylated group is covalently bound to Cys 8 to form a cyclic peptide. The peptide is terminated with an ...Details: Chains C and D are an N-terminal acetylated peptide with a D-Tyr at position 1. The acetylated group is covalently bound to Cys 8 to form a cyclic peptide. The peptide is terminated with an NH2 group. Ac(DTY)DYPGDFCYLYNH2
Source: (synth.) Caenorhabditis elegans (invertebrata)

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Non-polymers , 4 types, 411 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.1 M Hepes, 3% (w/v) Trimethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.69 Å / Num. obs: 64166 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.9 / Num. measured all: 219493 / Scaling rejects: 95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.1-2.153.40.5811546044960.7832.199.9
9.62-44.693.30.0323176940.99827.696.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.97 Å44.69 Å
Translation6.97 Å44.69 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18rc1_3769refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KGN

5kgn


Resolution: 2.1→44.69 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 3104 4.84 %
Rwork0.1667 61047 -
obs0.1693 64151 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.02 Å2 / Biso mean: 30.8718 Å2 / Biso min: 16.62 Å2
Refinement stepCycle: final / Resolution: 2.1→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8049 0 12 399 8460
Biso mean--32.79 34.18 -
Num. residues----1071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.130.32521490.226827212870100
2.13-2.170.2971650.218827482913100
2.17-2.210.3111330.208327652898100
2.21-2.250.26581140.207728132927100
2.25-2.290.26781320.199327492881100
2.29-2.340.22971420.189527652907100
2.34-2.390.26371300.18227832913100
2.39-2.440.24161350.174327582893100
2.44-2.50.27941410.173827602901100
2.5-2.570.23981400.169627952935100
2.57-2.650.21051410.165627782919100
2.65-2.730.21991530.16527602913100
2.73-2.830.22371490.165727612910100
2.83-2.940.21391220.169828002922100
2.94-3.080.23161560.179427782934100
3.08-3.240.22231310.180127602891100
3.24-3.440.2281410.169927952936100
3.44-3.710.21581530.15982759291299
3.71-4.080.21450.14472780292599
4.08-4.670.16271440.13182783292799
4.67-5.880.1791440.1422796294099
5.88-44.690.19861440.16852840298498

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