[English] 日本語
Yorodumi
- PDB-4gm2: The crystal structure of a peptidase from plasmodium falciparum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gm2
TitleThe crystal structure of a peptidase from plasmodium falciparum
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / Protease
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 / serine-type endopeptidase activity / proteolysis
Similarity search - Function
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 / molecular replacement / Resolution: 2.8 Å
AuthorsEl Bakkouri, M. / Jung, P. / Wernimont, A.K. / Calmettes, C. / Hui, R. / Houry, W.A. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Insights into the Inactive Subunit of the Apicoplast-localized Caseinolytic Protease Complex of Plasmodium falciparum.
Authors: El Bakkouri, M. / Rathore, S. / Calmettes, C. / Wernimont, A.K. / Liu, K. / Sinha, D. / Asad, M. / Jung, P. / Hui, R. / Mohmmed, A. / Houry, W.A.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _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


Theoretical massNumber of molelcules
Total (without water)164,0367
Polymers164,0367
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13190 Å2
ΔGint-57 kcal/mol
Surface area55760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.898, 102.162, 96.414
Angle α, β, γ (deg.)90.000, 114.530, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 61 - 243 / Label seq-ID: 22 - 204

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17BB
27CC
18BB
28DD
19BB
29EE
110BB
210FF
111BB
211GG
112CC
212DD
113CC
213EE
114CC
214FF
115CC
215GG
116DD
216EE
117DD
217FF
118DD
218GG
119EE
219FF
120EE
220GG
121FF
221GG

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

-
Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit


Mass: 23433.678 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF14_0348 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): SG1146 / References: UniProt: Q8IL98
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TrisHCl, 20% (v/v) ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 39735 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Χ2: 1.196 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.853.80.75519770.7541100
2.85-2.93.80.60419890.7291100
2.9-2.963.80.50919480.7621100
2.96-3.023.80.40220100.7871100
3.02-3.083.80.33619760.8051100
3.08-3.153.80.25719790.8361100
3.15-3.233.80.20319680.8371100
3.23-3.323.80.17119780.8551100
3.32-3.423.80.12319790.8961100
3.42-3.533.80.09920070.892199.9
3.53-3.653.80.08119660.9571100
3.65-3.83.80.06419911.01199.9
3.8-3.973.80.05419841.0541100
3.97-4.183.80.04320031.0711100
4.18-4.443.80.03719661.1831100
4.44-4.793.80.03919961.4051100
4.79-5.273.80.04319901.6671100
5.27-6.033.70.0520171.9841100
6.03-7.593.70.03620131.9551100
7.59-503.50.02819983.857197.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2323 / WRfactor Rwork: 0.2012 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8425 / SU B: 29.441 / SU ML: 0.264 / SU R Cruickshank DPI: 0.2929 / SU Rfree: 0.3296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2006 5 %RANDOM
Rwork0.1991 ---
obs0.2007 39735 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.93 Å2 / Biso mean: 101.045 Å2 / Biso min: 43.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å22.04 Å2
2---1.33 Å20 Å2
3---3.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9542 0 0 69 9611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.029688
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.97213078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.87651190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1925.613408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.255151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6591525
X-RAY DIFFRACTIONr_chiral_restr0.0680.21551
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026946
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A2450.11
12B2450.11
21A2460.1
22C2460.1
31A2460.1
32D2460.1
41A2650.06
42E2650.06
51A2560.06
52F2560.06
61A2550.07
62G2550.07
71B2410.12
72C2410.12
81B2470.1
82D2470.1
91B2490.12
92E2490.12
101B2520.11
102F2520.11
111B2470.12
112G2470.12
121C2370.08
122D2370.08
131C2470.09
132E2470.09
141C2470.11
142F2470.11
151C2460.08
152G2460.08
161D2500.11
162E2500.11
171D2500.11
172F2500.11
181D2460.09
182G2460.09
191E2590.1
192F2590.1
201E2580.09
202G2580.09
211F2560.09
212G2560.09
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 151 -
Rwork0.28 2675 -
all-2826 -
obs--96.35 %
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)
12.883-0.3125-1.02372.944-0.08663.2054-0.1753-0.3732-0.39460.24450.0365-0.23860.3005-0.16190.13880.085-0.0239-0.00380.2090.06960.08345.211110.646722.3762
23.46220.8719-0.03375.3062-1.03854.3538-0.0717-0.6477-0.30290.8693-0.2325-0.6892-0.57540.50480.30420.279-0.1395-0.13780.31060.05990.199957.364649.947319.3681
34.881-0.8158-0.18023.16150.28392.947-0.132-0.5313-0.33960.69460.0854-0.02960.33210.11390.04660.24270.07060.02110.11130.09530.131333.37834.173715.0319
47.8049-0.0435-0.54785.53441.48813.87830.0028-0.93650.78080.697-0.06220.3699-0.2955-0.18360.05940.38380.1136-0.00410.2616-0.10890.45716.310260.607527.4767
55.84820.32691.17862.99521.59343.9631-0.4635-0.64690.60470.15890.17450.2145-0.3558-0.03650.2890.39650.0616-0.06770.1157-0.03010.236.711866.512227.4271
64.69240.882-0.01986.4488-1.07752.75230.1375-0.4483-0.29140.6753-0.1662-1.34180.20530.54280.02870.12070.0696-0.17070.24190.01770.327157.322420.198913.7292
74.06630.3225-0.54833.83540.37123.77040.1037-0.15830.45240.5525-0.050.3094-0.2224-0.4254-0.05370.13950.10470.07090.30610.01590.0792-6.57235.606125.4355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 243
2X-RAY DIFFRACTION2B61 - 243
3X-RAY DIFFRACTION3C61 - 243
4X-RAY DIFFRACTION4D61 - 243
5X-RAY DIFFRACTION5E61 - 243
6X-RAY DIFFRACTION6F61 - 243
7X-RAY DIFFRACTION7G61 - 243

+
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