[English] 日本語
Yorodumi
- PDB-8v5c: IpaD (122-321) Bound to Deoxycholate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v5c
TitleIpaD (122-321) Bound to Deoxycholate
ComponentsInvasin IpaD
KeywordsCELL INVASION / T3SS / Shigella / Pi-helix / Deoxycholate
Function / homologyeffector-mediated activation of programmed cell death in host / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / extracellular region / Invasin IpaD
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBarker, S.A. / Dickenson, N.E. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and functional characterization of the IpaD pi-helix reveals critical roles in DOC interaction, T3SS apparatus maturation, and Shigella virulence.
Authors: Barker, S.A. / Bernard, A.R. / Morales, Y. / Johnson, S.J. / Dickenson, N.E.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Invasin IpaD
B: Invasin IpaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0166
Polymers44,0472
Non-polymers9694
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-14 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.768, 43.350, 93.439
Angle α, β, γ (deg.)90.00, 97.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Invasin IpaD


Mass: 22023.537 Da / Num. of mol.: 2 / Fragment: residues 122-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.018 - 0.02 M Magnesium Chloride Hexahydrate, 20% w/v Poly(acrylic acid sodium salt) 5100, 0.3 mM Deoxycholate acid sodium salt

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.96→35 Å / Num. obs: 35366 / % possible obs: 97.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Χ2: 1.014 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.96-2.035.60.33332430.9480.9870.1450.3651.03190.8
2.03-2.1160.27934790.9610.990.1190.3041.03196.5
2.11-2.216.10.22134730.9730.9930.0950.2421.05396
2.21-2.326.90.19435650.9810.9950.0780.211.02798.6
2.32-2.476.90.16535420.9810.9950.0670.1781.02698.4
2.47-2.666.90.14535980.9820.9950.0590.1571.00499.1
2.66-2.936.60.1335480.9870.9970.0540.1410.99297.4
2.93-3.357.10.11136400.9860.9960.0450.121.00999.3
3.35-4.226.70.09435640.9910.9980.0390.1020.98997.6
4.22-356.90.07837140.9940.9990.0320.0850.9998.4

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→34.057 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 1762 5 %
Rwork0.1886 --
obs0.1904 35231 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→34.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 68 153 3171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093067
X-RAY DIFFRACTIONf_angle_d1.0014156
X-RAY DIFFRACTIONf_dihedral_angle_d4.4811824
X-RAY DIFFRACTIONf_chiral_restr0.056474
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0130.26311240.23892346X-RAY DIFFRACTION90
2.013-2.07220.27911320.23312520X-RAY DIFFRACTION95
2.0722-2.13910.28651330.21432523X-RAY DIFFRACTION98
2.1391-2.21550.23991320.20712513X-RAY DIFFRACTION96
2.2155-2.30420.24861360.19562592X-RAY DIFFRACTION99
2.3042-2.40910.24671380.19642613X-RAY DIFFRACTION99
2.4091-2.5360.23221380.18882617X-RAY DIFFRACTION99
2.536-2.69490.24641360.19552594X-RAY DIFFRACTION99
2.6949-2.90280.24461350.20192555X-RAY DIFFRACTION97
2.9028-3.19480.2661380.20362628X-RAY DIFFRACTION99
3.1948-3.65660.23921400.19642644X-RAY DIFFRACTION99
3.6566-4.60510.18781370.16252613X-RAY DIFFRACTION97
4.6051-34.0570.19271430.17922711X-RAY DIFFRACTION98
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)
10.64540.3277-0.45071.0593-0.90696.41510.06080.039-0.0182-0.0846-0.0845-0.0834-0.27510.42050.02660.39760.04020.01640.1942-0.01920.3439-29.9342-6.717426.6635
20.74090.026-0.1791.5664-0.00257.5122-0.00760.18430.0553-0.19510.1111-0.15860.25630.8037-0.09450.40410.03530.04590.253-0.02880.3205-24.8791-8.94813.8814
33.77992.92224.24753.54963.16827.21930.115-0.27520.15670.6283-0.23810.2744-0.2098-0.47370.17540.48220.00930.09520.1955-0.00170.3074-41.3254-19.155150.771
43.76762.28734.44371.93161.34728.34250.30430.8477-0.5726-0.4549-0.36260.62080.7736-1.3574-0.0470.65080.0861-0.20361.094-0.37590.8144-62.8582-26.290214.8217
58.4699-3.1902-1.1782.7284-3.04678.354-0.07530.0851-0.13620.41610.07430.3654-0.6878-1.42890.04240.4980.1683-0.08460.6876-0.13770.543-62.3224-15.772228.8541
61.43460.46992.27285.1467-0.60663.9284-0.19990.7878-0.152-0.41780.27340.6003-1.29510.41260.14690.98850.3256-0.2811.6645-0.39670.8444-68.9738-16.8861.4116
76.82611.14944.73352.4522.2528.49910.09231.26530.0911-0.8181-0.37320.3048-0.13620.27990.03470.57060.1296-0.03180.4198-0.03440.3329-48.3493-20.202918.637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 122 through 186 )
2X-RAY DIFFRACTION2chain 'A' and (resid 187 through 320 )
3X-RAY DIFFRACTION3chain 'B' and (resid 123 through 149 )
4X-RAY DIFFRACTION4chain 'B' and (resid 150 through 205 )
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 250 )
6X-RAY DIFFRACTION6chain 'B' and (resid 251 through 274 )
7X-RAY DIFFRACTION7chain 'B' and (resid 275 through 319 )

+
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://pdbjlc1.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