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- PDB-6a9v: Crystal structure of Icp55 from Saccharomyces cerevisiae (N-termi... -

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Basic information

Entry
Database: PDB / ID: 6a9v
TitleCrystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 42 residues deletion)
ComponentsIntermediate cleaving peptidase 55
KeywordsHYDROLASE / Intermediate cleaving peptidase 55 / M24B / peptidase / Xaa-Pro aminopeptidase / mitochondrial
Function / homology
Function and homology information


intermediate cleaving peptidase 55 / metalloaminopeptidase activity / aminopeptidase activity / protein processing / manganese ion binding / mitochondrial inner membrane / protein stabilization / mitochondrion / proteolysis / nucleus
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GLYCINE / : / TRIETHYLENE GLYCOL / Intermediate cleaving peptidase 55
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsSingh, R. / Kumar, A. / Goyal, V.D. / Makde, R.D.
CitationJournal: FEBS Lett. / Year: 2019
Title: Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function.
Authors: Singh, R. / Goyal, V.D. / Kumar, A. / Sabharwal, N.S. / Makde, R.D.
History
DepositionJul 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intermediate cleaving peptidase 55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3595
Polymers53,0241
Non-polymers3354
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, On Superdex200, elutes at a volume which corresponds to molecular mass of 74 kDa (equillibration between monomer and dimer). PISA analysis suggests monomeric nature of protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint2 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.081, 142.081, 118.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Intermediate cleaving peptidase 55 / / Intermediate cleaving peptidase of 55 kDa


Mass: 53023.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ICP55, YER078C / Plasmid: pST50STR / Details (production host): pET expression palsmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P40051, intermediate cleaving peptidase 55
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2

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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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 100mM HEPES pH 7.5, 22 % Peg3350 , 250mM Ammonium Sulphate, 0.2mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 17, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.9→45.554 Å / Num. obs: 13770 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.056 / Rrim(I) all: 0.166 / Net I/σ(I): 15.2
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2173 / CC1/2: 0.775 / Rpim(I) all: 0.374 / Rrim(I) all: 1.125 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementResolution: 2.9→45.554 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 734 5.34 %
Rwork0.213 --
obs0.2137 13751 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 17 0 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023184
X-RAY DIFFRACTIONf_angle_d0.464304
X-RAY DIFFRACTIONf_dihedral_angle_d12.4741921
X-RAY DIFFRACTIONf_chiral_restr0.041477
X-RAY DIFFRACTIONf_plane_restr0.004560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.12410.31711420.30222533X-RAY DIFFRACTION100
3.1241-3.43840.27451600.25762555X-RAY DIFFRACTION100
3.4384-3.93570.21481420.21632587X-RAY DIFFRACTION100
3.9357-4.95760.21081350.17332628X-RAY DIFFRACTION100
4.9576-45.55930.19081550.20352714X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -10.5926 Å / Origin y: -35.3709 Å / Origin z: -16.5881 Å
111213212223313233
T0.3753 Å20.0492 Å2-0.079 Å2-0.2702 Å20.0032 Å2--0.3368 Å2
L2.0173 °20.8347 °2-0.1786 °2-0.8824 °20.2375 °2--1.3674 °2
S-0.0765 Å °-0.0503 Å °-0.0124 Å °0.0463 Å °0.0145 Å °-0.0516 Å °0.1409 Å °0.0707 Å °0.0519 Å °
Refinement TLS groupSelection details: all

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