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- PDB-7knf: 1.80A resolution structure of independent Phosphoglycerate mutase... -

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Basic information

Entry
Database: PDB / ID: 7knf
Title1.80A resolution structure of independent Phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Ce-1 NHOH)
Components
  • 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
  • DTY-ASP-TYR-PRO-GLY-ASP-HIS-CYS-TYR-LEU-TYR-GLY-THR
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
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 speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 2.0Feb 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.entity_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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


Theoretical massNumber of molelcules
Total (without water)122,73215
Polymers121,7964
Non-polymers93611
Water13,493749
1
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
C: DTY-ASP-TYR-PRO-GLY-ASP-HIS-CYS-TYR-LEU-TYR-GLY-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4638
Polymers60,8982
Non-polymers5656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-70 kcal/mol
Surface area19720 Å2
MethodPISA
2
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
D: DTY-ASP-TYR-PRO-GLY-ASP-HIS-CYS-TYR-LEU-TYR-GLY-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2697
Polymers60,8982
Non-polymers3715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-70 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.669, 75.846, 100.424
Angle α, β, γ (deg.)90.000, 98.310, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-961-

HOH

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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: 59289.102 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-HIS-CYS-TYR-LEU-TYR-GLY-THR


Mass: 1608.708 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 NH-OH group. AcDYDYPGDHCYLYGT-NH-OH
Source: (synth.) Caenorhabditis elegans (invertebrata)

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Non-polymers , 4 types, 760 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.6 Å / Num. obs: 101405 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2 / Num. measured all: 767614 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.8-1.837.51.2173695849110.7351.899.8
9.86-48.67.40.04749236610.99835.398.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5kgn


Resolution: 1.8→44.13 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 5040 4.97 %
Rwork0.1521 96340 -
obs0.1542 101380 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.89 Å2 / Biso mean: 24.1408 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 1.8→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7860 0 42 749 8651
Biso mean--33.58 32.21 -
Num. residues----1039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.820.30021320.240731843316
1.82-1.840.27911880.232832023390
1.84-1.860.2331880.214531353323
1.86-1.890.25091790.208232093388
1.89-1.910.26081670.202831513318
1.91-1.940.24381740.194432253399
1.94-1.970.22341580.188731893347
1.97-20.2261570.177732563413
2-2.030.2261760.167931483324
2.03-2.060.21361870.16731833370
2.06-2.10.20971710.162732203391
2.1-2.130.21841670.159331613328
2.13-2.180.19251900.146531963386
2.18-2.220.19091730.146231893362
2.22-2.270.1891630.143432123375
2.27-2.320.22371650.148132003365
2.32-2.380.1891890.143432043393
2.38-2.440.19411420.137932163358
2.44-2.510.16261880.136632313419
2.51-2.60.16571490.135231863335
2.6-2.690.20021590.138932223381
2.69-2.80.19921730.140932203393
2.8-2.920.21511740.145732103384
2.92-3.080.20251720.14532103382
3.08-3.270.19571670.15632103377
3.27-3.520.18231520.148532753427
3.52-3.880.16161600.137632403400
3.88-4.440.15961750.120832403415
4.44-5.590.1451550.130932733428
5.59-44.130.22421500.185533433493

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