[English] 日本語
Yorodumi
- PDB-7kld: Crystal Structure of an Essential Ribosomal Processing Protease P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kld
TitleCrystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in complex with a covalently linked product Peptide
Components
  • LYS-LEU-ASN-LEU-GLN-PHE-PCS
  • Phage-related ribosomal protease
KeywordsHYDROLASE / cysteine protease ribosomal protein L27 / product complex
Function / homologyCysteine protease Prp / Cysteine protease Prp superfamily / Cysteine protease Prp / cysteine-type peptidase activity / ribosome / proteolysis / : / Ribosomal processing cysteine protease Prp
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWright, H.T. / Peterson, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21: NIH R21 AI109202 United States
CitationJournal: Biochemistry / Year: 2022
Title: Phage-Related Ribosomal Protease (Prp) of Staphylococcus aureus : In Vitro Michaelis-Menten Kinetics, Screening for Inhibitors, and Crystal Structure of a Covalent Inhibition Product Complex.
Authors: Hotinger, J.A. / Pendergrass, H.A. / Peterson, D. / Wright, H.T. / May, A.E.
History
DepositionOct 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phage-related ribosomal protease
B: Phage-related ribosomal protease
C: LYS-LEU-ASN-LEU-GLN-PHE-PCS
D: Phage-related ribosomal protease
E: LYS-LEU-ASN-LEU-GLN-PHE-PCS
Q: LYS-LEU-ASN-LEU-GLN-PHE-PCS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25414
Polymers37,9336
Non-polymers3218
Water1,56787
1
A: Phage-related ribosomal protease
B: Phage-related ribosomal protease
C: LYS-LEU-ASN-LEU-GLN-PHE-PCS
Q: LYS-LEU-ASN-LEU-GLN-PHE-PCS
hetero molecules

A: Phage-related ribosomal protease
B: Phage-related ribosomal protease
C: LYS-LEU-ASN-LEU-GLN-PHE-PCS
Q: LYS-LEU-ASN-LEU-GLN-PHE-PCS
hetero molecules

D: Phage-related ribosomal protease
E: LYS-LEU-ASN-LEU-GLN-PHE-PCS
hetero molecules

D: Phage-related ribosomal protease
E: LYS-LEU-ASN-LEU-GLN-PHE-PCS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,50828
Polymers75,86612
Non-polymers64116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_444x-1/2,y-1/2,z-1/21
crystal symmetry operation4_545-x+1/2,y-1/2,-z+1/21
Buried area15200 Å2
ΔGint-223 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.482, 66.556, 93.446
Angle α, β, γ (deg.)90.000, 103.438, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

#1: Protein Phage-related ribosomal protease / Ribosomal-processing cysteine protease Prp / Ribosome-associated protein


Mass: 11701.829 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Electron density is missing for residues 24 - 29 in chain A
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: BN1321_260284, BTN44_03930, C7P97_01985, CSC87_06715, DD547_01729, DDL17_04735, DQV20_11645, DQV53_09155, E3A28_00240, E3K14_08315, E4U00_05990, EP54_09330, EQ90_02345, ERS072840_00776, FA040_ ...Gene: BN1321_260284, BTN44_03930, C7P97_01985, CSC87_06715, DD547_01729, DDL17_04735, DQV20_11645, DQV53_09155, E3A28_00240, E3K14_08315, E4U00_05990, EP54_09330, EQ90_02345, ERS072840_00776, FA040_12870, FVP29_06750, G0V24_11265, G0X12_13445, G0X27_07880, G0Y02_04565, G0Z08_03095, G0Z18_03180, G6W67_00930, G6W97_12315, G6X24_04030, G6X31_01365, G6X35_09650, G6Y10_03065, G6Y24_01400, G6Y28_11445, G6Y30_16890, GF545_03610, GF559_00535, GIX97_04380, GO677_13485, GO706_06595, GO746_11035, GO788_00935, GO793_02925, GO793_12515, GO803_01985, GO805_05045, GO810_16085, GO821_00235, GO894_13395, GO915_03870, GO941_09805, GO942_04925, HMPREF3211_01798, M1K003_1397, NCTC10654_01710, NCTC10702_02585, NCTC5664_03624, NCTC6133_02188, NCTC7878_03165, RK64_08805, SAMEA1029528_01686, SAMEA1029547_02076, SAMEA1029553_02519, SAMEA1469856_00607, SAMEA1469884_01223, SAMEA1531680_00288, SAMEA1531701_01205, SAMEA1964876_02447, SAMEA1965205_02481, SAMEA1966505_02490, SAMEA1969349_02416, SAMEA1969845_01676, SAMEA1971706_01055, SAMEA1972827_01838, SAMEA2076212_01600, SAMEA2076218_01666, SAMEA2076220_01752, SAMEA2076226_01556, SAMEA2076463_02381, SAMEA2076464_02394, SAMEA2076470_02431, SAMEA2076472_02346, SAMEA2076478_02402, SAMEA2076480_02456, SAMEA2076481_02468, SAMEA2076743_02501, SAMEA2076745_02445, SAMEA2076746_02444, SAMEA2076747_02486, SAMEA2076749_02400, SAMEA2076751_02425, SAMEA2076752_02493, SAMEA2076755_02464, SAMEA2076756_02514, SAMEA2076758_02521, SAMEA2076759_02515, SAMEA2076761_02557, SAMEA2076762_01945, SAMEA2076763_01877, SAMEA2076764_02486, SAMEA2076765_02396, SAMEA2077023_02451, SAMEA2077025_02500, SAMEA2077027_02451, SAMEA2077029_02463, SAMEA2077031_02497, SAMEA2077034_01994, SAMEA2077035_02483, SAMEA2077039_02486, SAMEA2077040_02404, SAMEA2077041_02447, SAMEA2077044_02452, SAMEA2077045_02427, SAMEA2077046_02417, SAMEA2077293_02510, SAMEA2077294_02438, SAMEA2077295_02425, SAMEA2077297_02396, SAMEA2077300_02477, SAMEA2077301_02476, SAMEA2077302_02443, SAMEA2077303_02458, SAMEA2077307_02357, SAMEA2077832_02485, SAMEA2078252_02489, SAMEA2078256_02457, SAMEA2078307_02502, SAMEA2078308_02409, SAMEA2078553_02399, SAMEA2078558_02472, SAMEA2078560_02496, SAMEA2078569_00046, SAMEA2078570_02413, SAMEA2078572_02514, SAMEA2078824_02435, SAMEA2078837_02548, SAMEA2079048_02570, SAMEA2079051_02465, SAMEA2079277_01808, SAMEA2079291_02682, SAMEA2079503_02553, SAMEA2079507_01005, SAMEA2079512_02667, SAMEA2079517_02674, SAMEA2079724_01337, SAMEA2079727_01612, SAMEA2079728_01943, SAMEA2079732_01656, SAMEA2079742_01684, SAMEA2079946_01624, SAMEA2079949_01591, SAMEA2079951_01555, SAMEA2079952_01419, SAMEA2079957_01912, SAMEA2079958_01822, SAMEA2079960_01835, SAMEA2079961_01609, SAMEA2079968_01340, SAMEA2080329_01468, SAMEA2080330_01912, SAMEA2080334_01932, SAMEA2080433_01740, SAMEA2080812_02522, SAMEA2080898_02518, SAMEA2080900_02445, SAMEA2080904_02459, SAMEA2080913_02507, SAMEA2081043_02492, SAMEA2081053_02569, SAMEA2081054_02533, SAMEA2081055_02521, SAMEA2081060_01823, SAMEA2081211_00857, SAMEA2081213_00881, SAMEA2081218_01649, SAMEA2081341_01341, SAMEA2081342_01612, SAMEA2081349_01864, SAMEA2081359_01619, SAMEA2081362_01623, SAMEA2081468_02419, SAMEA2081474_02496, SAMEA2081475_02467, SAMEA2081476_02433, SAMEA2081479_02517, SAMEA2081480_02464, SAMEA2081560_02361, SAMEA2081561_02437, SAMEA2081564_02416, SAMEA2081567_02404, SAMEA2081568_02500, SAMEA2081569_02476, SAMEA2081570_02367, SAMEA2081571_02441, SAMEA2081572_02441, SAMEA2081573_02444, SAMEA2081575_02417, SAMEA2081577_02472, SAMEA2081578_02440, SAMEA2081579_02464, SAMEA2081581_02376, SAMEA2081582_02553, SAMEA2081673_01456, SAMEA2081674_01693, SAMEA958766_01141, SAMEA958770_01541, SAMEA958772_01367, SAMEA958778_01377, SAMEA958779_02720, SAMEA958785_01190, SAMEA958793_01565, SAMEA958798_01254, SAMEA958804_01429, SAMEA958810_02901, SAMEA958836_01614, SAMEA958838_02812, SAMEA958845_01498, SAMEA958846_01744, SAMEA958848_02333, SAMEA958855_02126, SAMEA958858_02293, SAMEA958870_02489, SAMEA958898_01783, SAMEA958906_02170, SAMEA958924_01277, SAMEA958925_01299, SAMEA958951_01296, SAMEA958953_00896, SAMEA958961_01996, SAMEA958979_01146, SAMEA958987_02151, SAMEA958995_01155, SAST44_01826, SAST45_01804
Plasmid: pEW34 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: W8U5D2
#2: Protein/peptide LYS-LEU-ASN-LEU-GLN-PHE-PCS


Type: Peptide-like / Class: Inhibitor / Mass: 942.562 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Amino terminal peptide of ribosomal protein L27 / Source: (synth.) Staphylococcus aureus (bacteria) / References: BIRD: PRD_002454
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.51 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein sample: 10 - 20 mg/ml in 10mM Hepes (pH 7.5), 0.1M NaCl, 0.3mM TCEP, 3.3mM Triss (pH 7.5), 0.5% beta-octylglucoside, <4% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 26, 2018 / Details: Rigaku Varimax-HF Arc
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.25→29.31 Å / Num. obs: 15213 / % possible obs: 95.2 % / Redundancy: 10.8 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 0.997 / R split: 0.062 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.047 / Rrim(I) all: 0.155 / Net I/av σ(I): 12.1 / Net I/σ(I): 3.84
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 14933 / CC1/2: 0.972 / Rpim(I) all: 0.19 / Rrim(I) all: 0.632 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrysalisPro40.64.42adata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PEO

4peo


Resolution: 2.25→29.31 Å / SU ML: 0.2131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 774 5.11 %
Rwork0.2455 14386 -
obs0.2472 15160 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.13 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 8 87 2608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01992526
X-RAY DIFFRACTIONf_angle_d1.83463451
X-RAY DIFFRACTIONf_chiral_restr0.1166415
X-RAY DIFFRACTIONf_plane_restr0.0106458
X-RAY DIFFRACTIONf_dihedral_angle_d17.8006886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.390.28631280.25822335X-RAY DIFFRACTION99
2.39-2.580.33121260.26362406X-RAY DIFFRACTION99.69
2.58-2.830.28481340.25682387X-RAY DIFFRACTION99.92
2.83-3.240.27731290.252400X-RAY DIFFRACTION100
3.24-4.080.26051220.22212416X-RAY DIFFRACTION99.57
4.09-29.310.27231350.24932442X-RAY DIFFRACTION99.27

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more