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- PDB-6a9u: Crystal strcture of Icp55 from Saccharomyces cerevisiae bound to ... -

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Basic information

Entry
Database: PDB / ID: 6a9u
TitleCrystal strcture of Icp55 from Saccharomyces cerevisiae bound to apstatin inhibitor
Components
  • Intermediate cleaving peptidase 55
  • apstatin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Intermediate cleaving peptidase 55 / M24B / peptidase / Xaa-Pro aminopeptidase / mitochondrial / Apstatin / N-((2S / 3R)-3-Amino-2-hydroxy-4-phenylbutanoyl)-Pro-Pro-Ala-NH2 / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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
APSTATIN / : / Intermediate cleaving peptidase 55
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _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
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intermediate cleaving peptidase 55
B: apstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9274
Polymers51,8172
Non-polymers1102
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibration between monomeric and dimeric form
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-19 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.089, 148.089, 124.989
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-762-

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 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: Protein/peptide apstatin


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 458.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: APSTATIN
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 100mM hipis pH 7 , 28% Jagffamine ED 2003 pH7, 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.4→47.76 Å / Num. obs: 27387 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 44.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.037 / Rrim(I) all: 0.101 / Net I/σ(I): 17.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2843 / CC1/2: 0.71 / Rpim(I) all: 0.487 / Rrim(I) all: 0.903 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A16

1a16


Resolution: 2.4→47.758 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.05
RfactorNum. reflection% reflection
Rfree0.2659 1407 5.14 %
Rwork0.2247 --
obs0.2268 27365 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 2 88 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043319
X-RAY DIFFRACTIONf_angle_d0.64488
X-RAY DIFFRACTIONf_dihedral_angle_d3.9462788
X-RAY DIFFRACTIONf_chiral_restr0.046494
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.48590.32261300.28312562X-RAY DIFFRACTION100
2.4859-2.58540.34891330.27992572X-RAY DIFFRACTION100
2.5854-2.7030.28481190.26772579X-RAY DIFFRACTION100
2.703-2.84550.34791380.26882571X-RAY DIFFRACTION100
2.8455-3.02380.34151540.26892560X-RAY DIFFRACTION100
3.0238-3.25720.36611440.27652566X-RAY DIFFRACTION100
3.2572-3.58490.28161480.23882604X-RAY DIFFRACTION100
3.5849-4.10340.27961590.20942581X-RAY DIFFRACTION100
4.1034-5.16890.18251450.16382639X-RAY DIFFRACTION100
5.1689-47.76730.21131370.21142724X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90092.10840.67252.36660.53591.82940.3379-0.6253-0.06580.4238-0.43710.03020.2432-0.54360.09930.3859-0.0256-0.04280.4799-0.01920.3141-26.5146-46.8757-7.8225
21.95470.53830.1951.09380.25162.4559-0.17310.12130.0074-0.10690.0969-0.1342-0.24050.33510.06180.35570.0017-0.09350.27080.01510.3711-0.296-30.1294-23.6725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 268 )
2X-RAY DIFFRACTION2chain 'A' and (resid 269 through 498 )

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