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- PDB-5kgn: 1.95A resolution structure of independent phosphoglycerate mutase... -

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Basic information

Entry
Database: PDB / ID: 5kgn
Title1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (2d)
Components
  • 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
  • macrocyclic peptide inhibitor
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) / 2,3-bisphosphoglycerate-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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: macrocyclic peptide inhibitor
D: macrocyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,87114
Polymers120,3264
Non-polymers54410
Water13,241735
1
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
C: macrocyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4357
Polymers60,1632
Non-polymers2725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-37 kcal/mol
Surface area20690 Å2
MethodPISA
2
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
D: macrocyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4357
Polymers60,1632
Non-polymers2725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-37 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.782, 75.832, 101.420
Angle α, β, γ (deg.)90.00, 95.66, 90.00
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: 58704.508 Da / Num. of mol.: 2 / Fragment: isoform b
Source method: isolated from a genetically manipulated source
Details: This form of the enzyme (M19 to I539, isoform b) is missing the first 18 residues relative to the full length sequence.
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: Protein/peptide macrocyclic peptide inhibitor


Mass: 1458.573 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This is a synthetically prepared peptide inhibitor. D-Tyrosine connected to the SG atom of Cys 8 by a thioether linkage to form the macrocyclic peptide.
Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 745 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.1 Tris, 0.2 M magnesium chloride

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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: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.17 Å / Num. obs: 80429 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.48 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 7.8
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.603 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.94 Å100.93 Å
Translation1.94 Å100.93 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.24data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KGL

5kgl


Resolution: 1.95→35.49 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 19.71
RfactorNum. reflection% reflection
Rfree0.204 4113 5.11 %
Rwork0.154 --
obs0.156 80411 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8179 0 20 735 8934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178451
X-RAY DIFFRACTIONf_angle_d0.89711436
X-RAY DIFFRACTIONf_dihedral_angle_d14.4313012
X-RAY DIFFRACTIONf_chiral_restr0.0731245
X-RAY DIFFRACTIONf_plane_restr0.0061510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.9730.26541460.21222551X-RAY DIFFRACTION98
1.973-1.9970.29811760.21072551X-RAY DIFFRACTION97
1.997-2.02230.28671460.20922624X-RAY DIFFRACTION99
2.0223-2.04890.25421360.1992585X-RAY DIFFRACTION97
2.0489-2.0770.21831520.1992562X-RAY DIFFRACTION98
2.077-2.10660.30451450.18422572X-RAY DIFFRACTION97
2.1066-2.13810.24471480.18212564X-RAY DIFFRACTION99
2.1381-2.17150.22691510.17352624X-RAY DIFFRACTION98
2.1715-2.20710.23971600.16522598X-RAY DIFFRACTION99
2.2071-2.24510.21371480.16232602X-RAY DIFFRACTION98
2.2451-2.28590.22031620.16142569X-RAY DIFFRACTION99
2.2859-2.32990.18351510.15382629X-RAY DIFFRACTION99
2.3299-2.37740.22531490.16062646X-RAY DIFFRACTION99
2.3774-2.42910.20851360.15072625X-RAY DIFFRACTION99
2.4291-2.48560.19591310.15092641X-RAY DIFFRACTION99
2.4856-2.54780.22041230.15152653X-RAY DIFFRACTION99
2.5478-2.61660.22031180.15332657X-RAY DIFFRACTION99
2.6166-2.69360.22611360.14822639X-RAY DIFFRACTION100
2.6936-2.78050.20141250.14492665X-RAY DIFFRACTION99
2.7805-2.87980.19351370.14842641X-RAY DIFFRACTION99
2.8798-2.99510.19521320.14452669X-RAY DIFFRACTION99
2.9951-3.13130.17661280.14682674X-RAY DIFFRACTION100
3.1313-3.29630.19821330.15082663X-RAY DIFFRACTION100
3.2963-3.50270.1811140.13912699X-RAY DIFFRACTION100
3.5027-3.77280.16221480.12962639X-RAY DIFFRACTION100
3.7728-4.1520.14761460.12212652X-RAY DIFFRACTION99
4.152-4.75160.15111440.11262669X-RAY DIFFRACTION99
4.7516-5.98180.18311230.15112713X-RAY DIFFRACTION99
5.9818-35.49970.23391690.19132722X-RAY DIFFRACTION99

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