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- PDB-6a9t: Crystal structure of Icp55 from Saccharomyces cerevisiae (N-termi... -

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Basic information

Entry
Database: PDB / ID: 6a9t
TitleCrystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 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 / cytosol
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 / Chem-JEF / : / Intermediate cleaving peptidase 55
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.2Nov 22, 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

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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)52,1415
Polymers51,3591
Non-polymers7834
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, equillibration between monomeric and dimeric forms
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.163, 141.163, 118.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-809-

HOH

21A-827-

HOH

31A-851-

HOH

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Components

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


Mass: 51358.691 Da / Num. of mol.: 1 / Mutation: D189E
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-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 100 mM HEPES, 30% Jeffamine ED2001, pH 7.0, 0.2 mM 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2014 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.15→45.35 Å / Num. obs: 31124 / % possible obs: 95.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Net I/σ(I): 23.1
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1901 / CC1/2: 0.69 / Rpim(I) all: 0.357 / Rrim(I) all: 0.92 / % possible all: 68.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A16

1a16


Resolution: 2.15→43.727 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.99
RfactorNum. reflection% reflection
Rfree0.2261 1592 5.12 %
Rwork0.1871 --
obs0.1891 31112 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→43.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 24 219 3486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023326
X-RAY DIFFRACTIONf_angle_d0.464499
X-RAY DIFFRACTIONf_dihedral_angle_d12.5152007
X-RAY DIFFRACTIONf_chiral_restr0.041501
X-RAY DIFFRACTIONf_plane_restr0.003588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.21950.3203930.25531923X-RAY DIFFRACTION69
2.2195-2.29890.241420.23852210X-RAY DIFFRACTION81
2.2989-2.39090.2541450.23052725X-RAY DIFFRACTION97
2.3909-2.49970.24371420.21392783X-RAY DIFFRACTION100
2.4997-2.63150.24311500.21362814X-RAY DIFFRACTION100
2.6315-2.79630.22831570.20492766X-RAY DIFFRACTION100
2.7963-3.01220.24271440.20112824X-RAY DIFFRACTION100
3.0122-3.31520.23491530.18782826X-RAY DIFFRACTION100
3.3152-3.79470.22511710.17242800X-RAY DIFFRACTION100
3.7947-4.780.1831470.15232868X-RAY DIFFRACTION100
4.78-43.73570.23161480.1862981X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -11.0431 Å / Origin y: -35.1892 Å / Origin z: -15.6558 Å
111213212223313233
T0.2961 Å20.0339 Å2-0.0573 Å2-0.2428 Å20.0026 Å2--0.2863 Å2
L2.1613 °21.1879 °20.3792 °2-1.3065 °20.3829 °2--1.3899 °2
S0.0502 Å °-0.1921 Å °-0.0268 Å °0.0697 Å °-0.1122 Å °-0.0223 Å °0.1309 Å °-0.0171 Å °0.0685 Å °
Refinement TLS groupSelection details: all

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