[English] 日本語
Yorodumi
- PDB-2f6i: Crystal structure of the ClpP protease catalytic domain from Plas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f6i
TitleCrystal structure of the ClpP protease catalytic domain from Plasmodium falciparum
ComponentsATP-dependent CLP protease, putative
KeywordsHYDROLASE / Clp protease / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


apicoplast / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / hydrolase activity / serine-type endopeptidase activity / proteolysis
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 speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMulichak, A. / Loppnau, P. / Bray, J. / Amani, M. / Vedadi, M. / Wasney, G. / Finerty, P. / Sundstrom, M. / Weigelt, J. / Edwards, A. ...Mulichak, A. / Loppnau, P. / Bray, J. / Amani, M. / Vedadi, M. / Wasney, G. / Finerty, P. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Hui, R. / Plotnikova, O. / Structural Genomics Consortium (SGC)
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: The Clp chaperones and proteases of the human malaria parasite Plasmodium falciparum.
Authors: El Bakkouri, M. / Pow, A. / Mulichak, A. / Cheung, K.L. / Artz, J.D. / Amani, M. / Fell, S. / de Koning-Ward, T.F. / Goodman, C.D. / McFadden, G.I. / Ortega, J. / Hui, R. / Houry, W.A.
#1: Journal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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, putative
B: ATP-dependent CLP protease, putative
C: ATP-dependent CLP protease, putative
D: ATP-dependent CLP protease, putative
E: ATP-dependent CLP protease, putative
F: ATP-dependent CLP protease, putative
G: ATP-dependent CLP protease, putative


Theoretical massNumber of molelcules
Total (without water)174,0947
Polymers174,0947
Non-polymers00
Water4,468248
1
A: ATP-dependent CLP protease, putative
B: ATP-dependent CLP protease, putative
C: ATP-dependent CLP protease, putative
D: ATP-dependent CLP protease, putative
E: ATP-dependent CLP protease, putative
F: ATP-dependent CLP protease, putative
G: ATP-dependent CLP protease, putative

A: ATP-dependent CLP protease, putative
B: ATP-dependent CLP protease, putative
C: ATP-dependent CLP protease, putative
D: ATP-dependent CLP protease, putative
E: ATP-dependent CLP protease, putative
F: ATP-dependent CLP protease, putative
G: ATP-dependent CLP protease, putative


Theoretical massNumber of molelcules
Total (without water)348,18814
Polymers348,18814
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area51810 Å2
ΔGint-261 kcal/mol
Surface area88350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.300, 196.460, 139.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetradecamer generated from the heptamer in the asymmetric unit by the operation: -X, Y, -Z+1/2

-
Components

#1: Protein
ATP-dependent CLP protease, putative


Mass: 24870.557 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pET-28a vector customized for thrombin cleavage and LIC
Production host: Escherichia coli (E. coli) / References: UniProt: O97252, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG MME 550, Ammonium sulfate, cacodylate buffer., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 78895 / Num. obs: 78895 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rsym value: 0.078
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.5 % / Num. unique all: 7777 / Rsym value: 0.316 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TYF

1tyf


Resolution: 2.45→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The following loops are unobserved and omitted from the model: Chain A 297-304, Chain B 290-304, Chain C 298-303, Chain D 297-303, Chain E 297-304, Chain F 292-303. Side chain atoms of ...Details: The following loops are unobserved and omitted from the model: Chain A 297-304, Chain B 290-304, Chain C 298-303, Chain D 297-303, Chain E 297-304, Chain F 292-303. Side chain atoms of residues listed in Remark 470 are unobserved in electron density maps and are omitted from model.
RfactorNum. reflectionSelection details
Rfree0.238 3790 random
Rwork0.21 --
all0.211 78853 -
obs0.211 76615 -
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9941 0 0 248 10189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.62

+
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://pdbjlvh1.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