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- PDB-6iqs: Crystal structure of Prc with L245A and L340G mutations in comple... -

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Basic information

Entry
Database: PDB / ID: 6iqs
TitleCrystal structure of Prc with L245A and L340G mutations in complex with NlpI
Components
  • Lipoprotein NlpI
  • Tail-specific protease
KeywordsHYDROLASE / protein quality control / peptidoglycan remodeling
Function / homology
Function and homology information


symbiont-mediated evasion of recognition by host complement / C-terminal processing peptidase / peptidoglycan metabolic process / protein catabolic process / outer membrane-bounded periplasmic space / protein-macromolecule adaptor activity / endopeptidase activity / cell division / serine-type endopeptidase activity / response to antibiotic ...symbiont-mediated evasion of recognition by host complement / C-terminal processing peptidase / peptidoglycan metabolic process / protein catabolic process / outer membrane-bounded periplasmic space / protein-macromolecule adaptor activity / 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 / PDZ domain / Tetratricopeptide repeat / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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: 2.69 Å
AuthorsChuech, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)222,6764
Polymers222,6764
Non-polymers00
Water91951
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)119.342, 144.415, 152.504
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
11SERSERLEULEUAA29 - 28329 - 283
21SERSERLEULEUBB29 - 28329 - 283
12ASPASPLYSLYSCC25 - 67125 - 671
22ASPASPLYSLYSDD25 - 67125 - 671

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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AFB1
#2: Protein Tail-specific protease / C-terminal-processing peptidase / PRC protein / Protease Re


Mass: 77496.672 Da / Num. of mol.: 2 / Mutation: L245A/L340G
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.: 51 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 27, 2018 / Details: Cryo-cooled channel-cut Si(111)
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. obs: 69840 / % possible obs: 94.7 % / Redundancy: 5 % / Biso Wilson estimate: 41.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.042 / Rrim(I) all: 0.098 / Χ2: 0.919 / Net I/σ(I): 13.47
Reflection shellResolution: 2.69→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.684 / Num. unique obs: 6187 / CC1/2: 0.783 / Rpim(I) all: 0.394 / Rrim(I) all: 0.813 / Χ2: 0.773 / % possible all: 85.1

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Processing

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

5wql


Resolution: 2.69→29.91 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 27.957 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.305 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24522 3435 5 %RANDOM
Rwork0.20496 ---
obs0.20695 65488 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.69→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12841 0 0 51 12892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01413086
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711718
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.65717697
X-RAY DIFFRACTIONr_angle_other_deg1.121.63927505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13451588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59922.622778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.916152322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1121599
X-RAY DIFFRACTIONr_chiral_restr0.10.21652
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022398
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_it3.0214.0786370
X-RAY DIFFRACTIONr_mcbond_other2.9764.0776369
X-RAY DIFFRACTIONr_mcangle_it4.836.1057952
X-RAY DIFFRACTIONr_mcangle_other4.8296.1067953
X-RAY DIFFRACTIONr_scbond_it3.0854.3286716
X-RAY DIFFRACTIONr_scbond_other3.0854.3296717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9776.3499746
X-RAY DIFFRACTIONr_long_range_B_refined8.94775.48955104
X-RAY DIFFRACTIONr_long_range_B_other8.94875.48955104
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)
11A90000.07
12B90000.07
21C174610.1
22D174610.1
LS refinement shellResolution: 2.688→2.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 195 -
Rwork0.317 3678 -
obs--71.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77720.1028-0.05490.999-0.0990.51560.00270.0141-0.0606-0.1119-0.0345-0.09630.11840.07360.03180.07470.01850.02320.03940.01320.054211.34618.481146.471
21.3969-0.04960.38590.74980.08390.5453-0.0204-0.08840.11070.0079-0.027-0.0267-0.08450.02390.04750.0511-0.00980.01920.0353-0.00050.05812.15649.319158.235
30.29220.1442-0.25550.1844-0.23410.79640.0236-0.11870.0397-0.045-0.05740.08040.08630.09820.03370.1852-0.01860.00090.0487-0.01750.07990.669-14.198180.47
40.1923-0.15920.04690.1706-0.1870.9343-0.00490.0602-0.03320.0232-0.05520.047-0.07380.04190.06010.24060.0107-0.0370.022-0.01650.08671.39582.167124.482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 92
2X-RAY DIFFRACTION1A93 - 173
3X-RAY DIFFRACTION1A174 - 196
4X-RAY DIFFRACTION1A197 - 281
5X-RAY DIFFRACTION1A282 - 284
6X-RAY DIFFRACTION2B28 - 92
7X-RAY DIFFRACTION2B93 - 173
8X-RAY DIFFRACTION2B174 - 196
9X-RAY DIFFRACTION2B197 - 281
10X-RAY DIFFRACTION2B282 - 286
11X-RAY DIFFRACTION3C25 - 232
12X-RAY DIFFRACTION3C343 - 379
13X-RAY DIFFRACTION3C380 - 563
14X-RAY DIFFRACTION3C564 - 675
15X-RAY DIFFRACTION4D27 - 232
16X-RAY DIFFRACTION4D343 - 379
17X-RAY DIFFRACTION4D380 - 563
18X-RAY DIFFRACTION4D564 - 672

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