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- PDB-6iqq: Crystal structure of Prc with S452I and L252Y mutations in comple... -

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Basic information

Entry
Database: PDB / ID: 6iqq
TitleCrystal structure of Prc with S452I and L252Y mutations in complex with NlpI
Components
  • Lipoprotein NlpI
  • Tail-specific protease
KeywordsHYDROLASE / protein quality control / peptidoglycan remodeling
Function / homology
Function and homology information


C-terminal processing peptidase / peptidoglycan metabolic process / cell outer membrane / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / receptor-mediated virion attachment to host cell / cell cycle / cell division ...C-terminal processing peptidase / peptidoglycan metabolic process / cell outer membrane / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / receptor-mediated virion attachment to host cell / cell cycle / cell division / response to antibiotic / serine-type endopeptidase activity / signal transduction / protein homodimerization activity / proteolysis / plasma membrane
Similarity search - Function
Tail specific protease, C-terminal / Lipoprotein NlpI / 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 / Tetratricopeptide repeat ...Tail specific protease, C-terminal / Lipoprotein NlpI / 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 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / ClpP/crotonase-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Lipoprotein NlpI / Tail-specific protease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChueh, C.K. / Chang, C.I.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)Non available 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

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein NlpI
B: Lipoprotein NlpI
C: Tail-specific protease
D: Tail-specific protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,1056
Polymers223,0254
Non-polymers802
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.936, 143.882, 153.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASPASPAA31 - 28631 - 286
21VALVALASPASPBB31 - 28631 - 286
12THRTHRGLUGLUCC27 - 67027 - 670
22THRTHRGLUGLUDD27 - 67027 - 670

NCS ensembles :
ID
1
2

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Components

#1: Protein Lipoprotein NlpI


Mass: 33841.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nlpI, yhbM, b3163, JW3132 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0AFB1
#2: Protein Tail-specific protease / C-terminal-processing peptidase / PRC protein / Protease Re


Mass: 77670.945 Da / Num. of mol.: 2 / Mutation: S452I, L252Y
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, Calcium acetate, Imidazole

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 25, 2017
Details: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 64129 / % possible obs: 98.3 % / Redundancy: 7.9 % / Biso Wilson estimate: 38.87 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.055 / Rrim(I) all: 0.154 / Χ2: 0.961 / Net I/σ(I): 13.92
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 6401 / CC1/2: 0.895 / Rpim(I) all: 0.263 / Rrim(I) all: 0.748 / Χ2: 0.86 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000v712data collection
Coot0.8.9.1model building
PHASER2.7.0phasing
HKL-2000V712data reduction
HKL-2000V712data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQL

5wql


Resolution: 2.8→29.98 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.861 / SU B: 14.126 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 1.634 / ESU R Free: 0.393 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27769 3248 5.1 %RANDOM
Rwork0.2215 ---
obs0.22442 60219 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.008 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.8→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14407 0 2 93 14502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01314668
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713693
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.64719832
X-RAY DIFFRACTIONr_angle_other_deg1.351.58331758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04551795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74422.627849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.349152622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.57615110
X-RAY DIFFRACTIONr_chiral_restr0.0870.21869
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023087
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_it6.6175.8617201
X-RAY DIFFRACTIONr_mcbond_other6.6165.8617200
X-RAY DIFFRACTIONr_mcangle_it9.9118.7728989
X-RAY DIFFRACTIONr_mcangle_other9.918.7738990
X-RAY DIFFRACTIONr_scbond_it6.2586.1347467
X-RAY DIFFRACTIONr_scbond_other6.2586.1347468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5719.01610844
X-RAY DIFFRACTIONr_long_range_B_refined14.68659862
X-RAY DIFFRACTIONr_long_range_B_other14.68659860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87250.09
12B87250.09
21C187350.15
22D187350.15
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 206 -
Rwork0.272 4002 -
obs--88.63 %

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