[English] 日本語
Yorodumi
- PDB-7ob6: CPR-C4 - a conserved novel protease from the Candidate Phyla Radiation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ob6
TitleCPR-C4 - a conserved novel protease from the Candidate Phyla Radiation
ComponentsCPR-C4
KeywordsHYDROLASE / Protease / cysteine protease / Zn
Biological speciescandidate division CPR1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.598 Å
AuthorsCornish, K.A.S. / Pohl, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: J.Biol.Chem. / Year: 2022
Title: CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins.
Authors: Cornish, K.A.S. / Lange, J. / Aevarsson, A. / Pohl, E.
History
DepositionApr 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CPR-C4
B: CPR-C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4794
Polymers54,3492
Non-polymers1312
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-75 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.392, 123.392, 96.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

21B-317-

HOH

31B-318-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A0 - 214
221B0 - 214

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein CPR-C4


Mass: 27174.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) candidate division CPR1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen (Molecular Dimensions)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763, 1.2824
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.28241
ReflectionResolution: 2.598→48.26 Å / Num. obs: 26494 / % possible obs: 99.8 % / Redundancy: 8.5 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.05 / Rrim(I) all: 0.106 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-48.267.80.01869410.0090.02
2.6-2.718.44.08631430.3682.1984.649

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
pointlessdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.598→46.791 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.209 / SU B: 17.956 / SU ML: 0.332 / Average fsc free: 0.7285 / Average fsc work: 0.7496 / Cross valid method: FREE R-VALUE / ESU R: 0.337 / ESU R Free: 0.278 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2853 1313 4.959 %
Rwork0.2344 25166 -
all0.237 --
obs-26479 99.751 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 102.186 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å21.71 Å20 Å2
2--3.42 Å2-0 Å2
3----11.093 Å2
Refinement stepCycle: LAST / Resolution: 2.598→46.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 2 63 3412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123445
X-RAY DIFFRACTIONr_ext_dist_refined_d0.3230.152047
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6314705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3315431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24821.905168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3931517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022659
X-RAY DIFFRACTIONr_nbd_refined0.2020.21433
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.289
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.25
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1720.21
X-RAY DIFFRACTIONr_mcbond_it8.96410.9581736
X-RAY DIFFRACTIONr_mcangle_it12.64616.4082163
X-RAY DIFFRACTIONr_scbond_it10.56710.8511709
X-RAY DIFFRACTIONr_scangle_it14.19416.2232542
X-RAY DIFFRACTIONr_lrange_it18.869404.32752464
X-RAY DIFFRACTIONr_ncsr_local_group_10.0720.056341
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.072040.05009
12BX-RAY DIFFRACTIONLocal ncs0.072040.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.598-2.6650.4651080.4531821X-RAY DIFFRACTION99.1774
2.665-2.7380.497940.4231775X-RAY DIFFRACTION99.7332
2.738-2.8180.3911020.4031725X-RAY DIFFRACTION99.6183
2.818-2.9040.421000.3831692X-RAY DIFFRACTION99.7773
2.904-2.9990.344800.3491640X-RAY DIFFRACTION99.6524
2.999-3.1050.341680.3091596X-RAY DIFFRACTION99.82
3.105-3.2220.383750.291546X-RAY DIFFRACTION99.8153
3.222-3.3530.349650.2581514X-RAY DIFFRACTION100
3.353-3.5020.283710.2391424X-RAY DIFFRACTION100
3.502-3.6730.308820.2131348X-RAY DIFFRACTION99.9301
3.673-3.8710.243570.21324X-RAY DIFFRACTION100
3.871-4.1060.24630.1831234X-RAY DIFFRACTION100
4.106-4.3890.271600.1811157X-RAY DIFFRACTION99.9179
4.389-4.740.2620.1781087X-RAY DIFFRACTION100
4.74-5.1910.325440.1971003X-RAY DIFFRACTION100
5.191-5.8020.289560.248911X-RAY DIFFRACTION99.8967
5.802-6.6960.268420.247817X-RAY DIFFRACTION100
6.696-8.1930.256460.205686X-RAY DIFFRACTION99.8636
8.193-11.5530.237280.168541X-RAY DIFFRACTION99.6497
11.553-46.7910.197100.275325X-RAY DIFFRACTION95.4416

+
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