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- PDB-6iqu: Crystal structure of Prc with PDZ domain deletion in complex with NlpI -

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Basic information

Entry
Database: PDB / ID: 6iqu
TitleCrystal structure of Prc with PDZ domain deletion 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 / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / cell division / serine-type endopeptidase activity / response to antibiotic / signal transduction ...C-terminal processing peptidase / peptidoglycan metabolic process / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / cell division / serine-type endopeptidase activity / response to antibiotic / 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 ...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 / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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: 2.9 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,8672
Polymers99,8672
Non-polymers00
Water19811
1
A: Lipoprotein NlpI
B: Tail-specific protease

A: Lipoprotein NlpI
B: Tail-specific protease


Theoretical massNumber of molelcules
Total (without water)199,7344
Polymers199,7344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)105.827, 151.082, 148.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Lipoprotein NlpI


Mass: 31865.410 Da / Num. of mol.: 1
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AFB1
#2: Protein Tail-specific protease / C-terminal-processing peptidase / PRC protein / Protease Re


Mass: 68001.547 Da / Num. of mol.: 1 / Mutation: G247~I338 deletion
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, sodium citrate tribasic dihydrate

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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: Sep 19, 2018
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: 2.9→50 Å / Num. obs: 25531 / % possible obs: 95.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.042 / Rrim(I) all: 0.088 / Χ2: 0.958 / Net I/σ(I): 18.95
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.39 / Num. unique obs: 1987 / CC1/2: 0.963 / Rpim(I) all: 0.141 / Rrim(I) all: 0.276 / Χ2: 0.874 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000V712data scaling
PHASER2.7phasing
Coot0.8.9.1model building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQL

5wql


Resolution: 2.9→38.8 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 13.737 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1192 5 %RANDOM
Rwork0.1919 ---
obs0.19398 22490 88.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.792 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.9→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6434 0 0 11 6445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136556
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176049
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.6488868
X-RAY DIFFRACTIONr_angle_other_deg1.2781.58214035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1865795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85522.748393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.522151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4571549
X-RAY DIFFRACTIONr_chiral_restr0.0730.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021396
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_it4.7345.1883189
X-RAY DIFFRACTIONr_mcbond_other4.7325.1883188
X-RAY DIFFRACTIONr_mcangle_it7.0827.7773981
X-RAY DIFFRACTIONr_mcangle_other7.0817.7773982
X-RAY DIFFRACTIONr_scbond_it4.785.4813366
X-RAY DIFFRACTIONr_scbond_other4.7695.4793364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1188.0644887
X-RAY DIFFRACTIONr_long_range_B_refined10.69396.5226932
X-RAY DIFFRACTIONr_long_range_B_other10.69296.5226933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.903→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 44 -
Rwork0.232 1072 -
obs--57.67 %

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