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- PDB-6iqr: Crystal structure of Prc with S452I and L252Y mutations -

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Basic information

Entry
Database: PDB / ID: 6iqr
TitleCrystal structure of Prc with S452I and L252Y mutations
ComponentsTail-specific protease
KeywordsHYDROLASE / protein quality control / peptidoglycan remodeling
Function / homology
Function and homology information


C-terminal processing peptidase / protein catabolic process / outer membrane-bounded periplasmic space / endopeptidase activity / response to antibiotic / serine-type endopeptidase activity / signal transduction / proteolysis / plasma membrane
Similarity search - Function
Tail specific protease, C-terminal / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / PDZ domain ...Tail specific protease, C-terminal / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Tail-specific protease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsChueh, C.K. / Chang, C.I.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Mbio / Year: 2019
Title: Structural Basis for the Differential Regulatory Roles of the PDZ Domain in C-Terminal Processing Proteases.
Authors: Chueh, C.K. / Som, N. / Ke, L.C. / Ho, M.R. / Reddy, M. / Chang, C.I.
History
DepositionNov 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail-specific protease
B: Tail-specific protease


Theoretical massNumber of molelcules
Total (without water)155,3422
Polymers155,3422
Non-polymers00
Water362
1
A: Tail-specific protease


Theoretical massNumber of molelcules
Total (without water)77,6711
Polymers77,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tail-specific protease


Theoretical massNumber of molelcules
Total (without water)77,6711
Polymers77,6711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.277, 129.277, 236.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 32 - 670 / Label seq-ID: 32 - 670

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Tail-specific protease / C-terminal-processing peptidase / PRC protein / Protease Re


Mass: 77670.945 Da / Num. of mol.: 2 / Mutation: L252Y/S452I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: prc, tsp, b1830, JW1819 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P23865, C-terminal processing peptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.68 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG3350, sodium thyocinate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 7, 2018
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.42→50 Å / Num. obs: 31494 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 44.65 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.069 / Rrim(I) all: 0.145 / Χ2: 0.968 / Net I/σ(I): 13.8
Reflection shellResolution: 3.42→3.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3117 / CC1/2: 0.772 / Rpim(I) all: 0.446 / Rrim(I) all: 0.942 / Χ2: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000v712data scaling
PHASER2.7phasing
Coot0.8.9.1model building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQL

5wql


Resolution: 3.42→29.97 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.79 / SU B: 18.879 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.631 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28758 1515 5.3 %RANDOM
Rwork0.23941 ---
obs0.24193 27244 90.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.348 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.42→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10143 0 0 2 10145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01410318
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179430
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.66313932
X-RAY DIFFRACTIONr_angle_other_deg0.9481.6422158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45451272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9622.192584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.799151892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1771585
X-RAY DIFFRACTIONr_chiral_restr0.0780.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021819
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.2817.0795097
X-RAY DIFFRACTIONr_mcbond_other8.2817.085096
X-RAY DIFFRACTIONr_mcangle_it13.07410.5896366
X-RAY DIFFRACTIONr_mcangle_other13.07310.5886367
X-RAY DIFFRACTIONr_scbond_it7.9667.6735221
X-RAY DIFFRACTIONr_scbond_other7.9647.6745219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.60711.3037566
X-RAY DIFFRACTIONr_long_range_B_refined25.93142474
X-RAY DIFFRACTIONr_long_range_B_other25.93142474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18589 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.42→3.509 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 51 -
Rwork0.128 939 -
obs--42.62 %

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