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- PDB-7tl7: 1.90A resolution structure of independent phosphoglycerate mutase... -

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Basic information

Entry
Database: PDB / ID: 7tl7
Title1.90A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Sa-D2)
Components
  • 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
  • peptide Sa-D2
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 / carbohydrate metabolic process / cytosol
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
: / IMIDAZOLE / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
C: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
D: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
a: peptide Sa-D2
b: peptide Sa-D2
c: peptide Sa-D2
d: peptide Sa-D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,02422
Polymers242,2718
Non-polymers75314
Water18,3931021
1
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
a: peptide Sa-D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7215
Polymers60,5682
Non-polymers1543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-67 kcal/mol
Surface area21350 Å2
MethodPISA
2
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
b: peptide Sa-D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7215
Polymers60,5682
Non-polymers1543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-68 kcal/mol
Surface area20640 Å2
MethodPISA
3
C: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
c: peptide Sa-D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7916
Polymers60,5682
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-69 kcal/mol
Surface area20640 Å2
MethodPISA
4
D: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
d: peptide Sa-D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7916
Polymers60,5682
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-65 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.999, 87.624, 151.341
Angle α, β, γ (deg.)90.000, 97.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDabcd

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


Mass: 58704.508 Da / Num. of mol.: 4 / 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
peptide Sa-D2


Type: Cyclic peptide / Class: Inhibitor / Mass: 1863.163 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: THIS IS A SYNTHETICALLY PREPARED PEPTIDE INHIBITOR. D-TYROSINE CONNECTED TO THE SG ATOM OF CYS 10 BY A THIOETHER LINKAGE TO FORM THE MACROCYCLIC PEPTIDE
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002491

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Non-polymers , 4 types, 1035 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MORPHEUS Screen Condition H4: 37.5% (w/v) of precipitant mix 4: (25% (v/v) MPD: 25% (w/v) PEG 1000: 25% (w/v) PEG 3350), 100 mM of MB1: (1.0 M imidazole, MES), 100 mM of MAA: (0.2 M DL- ...Details: MORPHEUS Screen Condition H4: 37.5% (w/v) of precipitant mix 4: (25% (v/v) MPD: 25% (w/v) PEG 1000: 25% (w/v) PEG 3350), 100 mM of MB1: (1.0 M imidazole, MES), 100 mM of MAA: (0.2 M DL-Glutamic acid monohydrate: 0.2 M DL-Alanine: 0.2M Glycine: 0.2 M DL-Lysine monohydrochloride: 0.2 M DL-Serine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.12 Å / Num. obs: 158753 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.8 / Num. measured all: 547906 / Scaling rejects: 50
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.9-1.933.50.7682752377830.6551.699.9
10.41-48.123.40.03349710260.9982798.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.20rc2_4402refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KGN

5kgn


Resolution: 1.9→39.84 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 7973 5.02 %
Rwork0.171 150706 -
obs0.1733 158679 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.26 Å2 / Biso mean: 29.8176 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: final / Resolution: 1.9→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16392 0 22 1021 17435
Biso mean--26.49 31.9 -
Num. residues----2160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.33352580.2749935251100
1.92-1.940.29952680.250950205288100
1.94-1.970.28422520.238449755227100
1.97-1.990.29052720.230150545326100
1.99-2.020.28492740.228650065280100
2.02-2.050.24962850.214549675252100
2.05-2.080.24632720.213449995271100
2.08-2.110.25742700.208250215291100
2.11-2.140.25032880.199149625250100
2.14-2.170.26472540.200950585312100
2.17-2.210.22582560.194450315287100
2.21-2.250.25932500.186849985248100
2.25-2.30.24872480.189250575305100
2.3-2.340.24482570.182149935250100
2.34-2.390.25312440.181650625306100
2.39-2.450.2472860.178650205306100
2.45-2.510.23212510.180450155266100
2.51-2.580.23422890.177249805269100
2.58-2.650.23262820.180850505332100
2.65-2.740.23612620.181650125274100
2.74-2.840.24792740.183650175291100
2.84-2.950.22942770.180350075284100
2.95-3.090.22322520.178650545306100
3.09-3.250.19712490.17825056530599
3.25-3.450.20222850.17074978526399
3.45-3.720.20492500.15265025527599
3.72-4.090.1732480.13565043529199
4.09-4.680.1422410.12085058529999
4.68-5.90.16662950.13595056535199
5.9-39.840.19622840.15955139542399

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