[English] 日本語
Yorodumi
- PDB-9cs7: Structure of Azospirillum bacterial CARD crystal form 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cs7
TitleStructure of Azospirillum bacterial CARD crystal form 1
ComponentsSerine protease
KeywordsIMMUNE SYSTEM / anti-phage defense / caspase activation and recruitment domain
Function / homologyPeptidase S1B / Trypsin-like peptidase domain / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / proteolysis / Serine protease
Function and homology information
Biological speciesAzospirillum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWein, T. / Millman, A. / Lange, K. / Yirmiya, E. / Hadary, R. / Garb, J. / Melamed, S. / Steinruecke, F. / HIll, A.B. / Kranzusch, P.J. / Sorek, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250 United States
Citation
Journal: Nature / Year: 2025
Title: CARD domains mediate anti-phage defence in bacterial gasdermin systems.
Authors: Wein, T. / Millman, A. / Lange, K. / Yirmiya, E. / Hadary, R. / Garb, J. / Melamed, S. / Amitai, G. / Dym, O. / Steinruecke, F. / Hill, A.B. / Kranzusch, P.J. / Sorek, R.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease
B: Serine protease


Theoretical massNumber of molelcules
Total (without water)23,3042
Polymers23,3042
Non-polymers00
Water1,71195
1
A: Serine protease


Theoretical massNumber of molelcules
Total (without water)11,6521
Polymers11,6521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease


Theoretical massNumber of molelcules
Total (without water)11,6521
Polymers11,6521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.959, 65.368, 38.831
Angle α, β, γ (deg.)90.000, 111.070, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Serine protease


Mass: 11652.190 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum (bacteria) / Gene: TSO352_05040 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2U1VUZ9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES-KOH (pH 7.5), 200 mM ammonium acetate, and 25% PEG-3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→36.24 Å / Num. obs: 14422 / % possible obs: 99.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.06 / Net I/σ(I): 7.7
Reflection shellResolution: 1.88→1.92 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 868 / CC1/2: 0.577 / Rpim(I) all: 0.775

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→36.23 Å / SU ML: 0.2536 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 1422 9.98 %
Rwork0.1979 12825 -
obs0.2014 14247 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.26 Å2
Refinement stepCycle: LAST / Resolution: 1.88→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 0 95 1682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221615
X-RAY DIFFRACTIONf_angle_d0.48722181
X-RAY DIFFRACTIONf_chiral_restr0.0349234
X-RAY DIFFRACTIONf_plane_restr0.0037290
X-RAY DIFFRACTIONf_dihedral_angle_d12.6925631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.940.35321230.30321154X-RAY DIFFRACTION88.13
1.94-2.020.30581430.23441256X-RAY DIFFRACTION97.02
2.02-2.110.26931430.21841291X-RAY DIFFRACTION98.42
2.11-2.230.28221430.19981294X-RAY DIFFRACTION99.79
2.23-2.370.22231410.20191298X-RAY DIFFRACTION99.45
2.37-2.550.2561440.20131295X-RAY DIFFRACTION98.97
2.55-2.80.24631490.2021287X-RAY DIFFRACTION99.58
2.8-3.210.22411420.1971293X-RAY DIFFRACTION99.24
3.21-4.040.22091470.17981316X-RAY DIFFRACTION99.86
4.04-36.230.19271470.1871341X-RAY DIFFRACTION99.6
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)
11.25552802291-0.127027486459-0.7318912874130.4367017351170.009536602527930.602710874492-0.138375668988-0.0434597038163-0.0670034257478-0.00855595946517-0.11262838351-0.01617228521340.2761350410360.157245658308-0.00755646089830.285727909624-0.02073309988270.03522282171860.1952598781820.0008303883357090.21053365097916.4478086894-1.244410699648.20021425622
20.7687903164920.149809617805-0.2723381793651.3538124649-1.119655909871.211181601790.4184712550080.3029554798190.0694514950232-0.289335862937-0.5426378792880.1152577322870.03749824877560.00118159192179-0.4505462882540.4673663940840.02661126930210.1120307392360.271059253128-0.08540379590530.2992111943543.14814010510.61828019161714.2276564439
30.8938834049490.01354167198180.1495505540750.431406771867-0.1930117274290.757505947006-0.295536980097-0.09358378430170.352075384401-0.1921984303820.02929055088960.306631525204-0.00348408172557-0.134524672029-0.06479300771470.301793034624-0.0495020733880.01893157061130.206311794773-0.02499501617490.2708409990647.594001248322.733264877316.40622712598
40.887981937587-0.7164303212130.7519047785060.875529858466-0.1771822850511.068240121510.1175094040620.1621092712660.134538662472-0.452913846427-0.0923529145929-0.5287882237950.07935675095910.400070082667-0.05915289846570.298414190433-0.008046541688090.07067917373940.2322013792680.02913431929520.21575192299323.0537036777-2.58757669854-1.01534865334
50.164402852161-0.133421590723-0.1731397727250.1636581314740.176736485460.3169776921440.2153786005920.0825292352420.12231028754-0.0696131708286-0.0683141947683-0.06575003874020.4433878101780.1551721936022.87838297195E-50.2950098725280.009012178946920.0203934695210.2730712885710.02367069087010.20648638437825.4529106062-21.58206843221.2312935053
60.09932370087220.183305479496-0.06644531148930.3971904185210.1143011729560.422199337490.1990688352490.1734435021080.112935888508-0.0703571251354-0.119712355478-0.0632367028305-0.1409206825060.05448731075130.01336038932980.2954029327180.006165803875350.08397227948520.2253716603650.006898045061190.23974468116129.3053058403-16.74943538976.82621954198
70.308705774756-0.258936441322-0.009672358192140.4785263405530.1010726565960.171154991238-0.00382806417957-0.154788613883-0.1465411240260.1719508209030.0948865770943-0.1658556923490.1734189066020.06964876284420.0008893437948930.3359409403160.04219926978560.0327767063510.2951839379620.01681022057990.28891717778630.5743942911-27.02985140512.2399221898
80.362851504673-0.21717828229-0.2185381350260.271234647034-0.16148487480.659644962422-0.1536799917520.1445013017560.3053734692540.4055885564920.2443226287010.0245987624792-0.335100158668-0.219455839860.003435169235760.337005407091-0.008262301979370.04007037331130.243657963198-0.003233467188590.30651735930524.4530394672-11.653672702219.2749158672
90.978124687766-0.586192095940.5926366807362.04614673457-0.7083371320451.85749524751-0.199674436164-0.803017040790.4273870190430.585909194490.5659333433440.0872271658976-0.72243010353-0.4814190416520.202828808240.5038855417530.0006194123726280.09775528510560.318147904371-0.003609849542830.24467304742318.0710874941-16.214972352328.0735342992
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 43 )AA12 - 431 - 32
22chain 'A' and (resid 44 through 57 )AA44 - 5733 - 46
33chain 'A' and (resid 58 through 79 )AA58 - 7947 - 68
44chain 'A' and (resid 80 through 110 )AA80 - 11069 - 99
55chain 'B' and (resid 12 through 24 )BB12 - 241 - 13
66chain 'B' and (resid 25 through 53 )BB25 - 5314 - 42
77chain 'B' and (resid 54 through 79 )BB54 - 7943 - 68
88chain 'B' and (resid 80 through 96 )BB80 - 9669 - 85
99chain 'B' and (resid 97 through 107 )BB97 - 10786 - 96

+
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