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- PDB-7kld: Crystal Structure of an Essential Ribosomal Processing Protease P... -

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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 / peptidase activity / ribosome / proteolysis / : / Predicted ribosomal protein
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Water


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

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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: 2.18 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

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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

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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

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