[English] 日本語
Yorodumi
- PDB-4jcr: ClpP1 N165D mutant from Listeria monocytogenes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jcr
TitleClpP1 N165D mutant from Listeria monocytogenes
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Pathogenic bacteria / Virulence factor / regulation / CLP protease family / active catalytic triad
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
Similarity search - Function
ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZeiler, E. / List, A. / Alte, F. / Gersch, M. / Wachtel, R. / Groll, M. / Sieber, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and functional insights into caseinolytic proteases reveal an unprecedented regulation principle of their catalytic triad.
Authors: Zeiler, E. / List, A. / Alte, F. / Gersch, M. / Wachtel, R. / Poreba, M. / Drag, M. / Groll, M. / Sieber, S.A.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit


Theoretical massNumber of molelcules
Total (without water)317,83614
Polymers317,83614
Non-polymers00
Water21,2761181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41990 Å2
ΔGint-195 kcal/mol
Surface area93180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.270, 147.410, 109.320
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.617441, 0.689364, -0.378872), (-0.665435, 0.714592, 0.215764), (0.419479, 0.118894, 0.899945)27.77944, 6.4496, -5.87357
3given(-0.215639, 0.880426, -0.422314), (-0.79934, 0.089248, 0.594214), (0.560853, 0.465708, 0.684514)50.40057, -8.2072, 0.9191
4given(-0.89816, 0.426261, -0.107748), (-0.303454, -0.42366, 0.85348), (0.318156, 0.799258, 0.509866)53.02569, -32.64094, 15.04654
5given(-0.891508, -0.315516, 0.325058), (0.437306, -0.412149, 0.799311), (-0.118223, 0.854742, 0.505411)32.35341, -49.09665, 26.24162
6given(-0.225339, -0.792145, 0.567211), (0.881478, 0.082219, 0.465013), (-0.414994, 0.604769, 0.679731)3.65158, -44.4061, 25.92725
7given(0.627164, -0.660623, 0.412604), (0.688199, 0.71808, 0.10365), (-0.364756, 0.218948, 0.904994)-10.1952, -22.07957, 13.70086
8given(0.892558, -0.433524, 0.124082), (-0.433101, -0.900785, -0.031787), (0.125552, -0.025368, -0.991763)-5.21574, -8.47989, 56.90971
9given(0.221479, -0.876646, 0.42713), (-0.87625, -0.371122, -0.307335), (0.427941, -0.306204, -0.850356)-3.52447, 15.86384, 42.67888
10given(-0.627305, -0.683735, 0.372819), (-0.685699, 0.257978, -0.680635), (0.369196, -0.682608, -0.630667)20.2933, 29.68507, 33.46141
11given(-0.999984, 0.005649, -0.000685), (0.003396, 0.495763, -0.868451), (-0.004567, -0.868439, -0.495774)47.79223, 21.65133, 36.38252
12given(-0.618869, 0.667687, -0.413757), (0.662594, 0.160843, -0.731505), (-0.421866, -0.726858, -0.541946)58.29715, -1.92961, 49.14059
13given(0.209144, 0.800947, -0.561019), (0.803146, -0.467981, -0.368714), (-0.557867, -0.373466, -0.741153)44.11512, -22.85497, 62.38254
14given(0.894622, 0.310315, -0.321491), (0.309943, -0.949235, -0.053748), (-0.321849, -0.05156, -0.945386)15.68684, -25.56694, 66.0715

-
Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 22702.602 Da / Num. of mol.: 14 / Mutation: N165D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: clpP, lmo1138 / Plasmid: pDEST GATEWAY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8Y7Y1, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1181 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1 M Tris, 0.2 M MgCl2, 16% PEG3350 , pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2012
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 177318 / Num. obs: 173949 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.5 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V5E

3v5e


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.258 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24294 8698 5 %RANDOM
Rwork0.21886 ---
all0.221 165250 --
obs0.22007 165250 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20.1 Å2
2--1.38 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19040 0 0 1181 20221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01919544
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.96226404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.35852408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.51625.152924
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.003153668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.39915126
X-RAY DIFFRACTIONr_chiral_restr0.0590.23080
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214434
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 621 -
Rwork0.285 11745 -
obs--97.8 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more