[English] 日本語
Yorodumi
- PDB-5vxk: 2.55 A resolution structure of IpaD from Shigella flexneri in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vxk
Title2.55 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-H2
Components
  • Invasin IpaD
  • single-domain antibody JMK-H2
KeywordsIMMUNE SYSTEM / tip protein / VHH / T3SS
Function / homology
Function and homology information


effector-mediated activation of programmed cell death in host / extracellular region
Similarity search - Function
IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.D. / Picking, W.L.
CitationJournal: To Be Published
Title: 2.55 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-H2
Authors: Barta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.D. / Picking, W.L.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: single-domain antibody JMK-H2
A: Invasin IpaD


Theoretical massNumber of molelcules
Total (without water)48,8202
Polymers48,8202
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.641, 107.913, 174.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Antibody single-domain antibody JMK-H2


Mass: 16914.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Invasin IpaD / 36 kDa membrane antigen


Mass: 31904.623 Da / Num. of mol.: 1 / Mutation: C322S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD, CP0126 / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride, 0.1 M Tris-HCl (pH 8.5), 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→45.88 Å / Num. obs: 17875 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Net I/σ(I): 14.8 / Num. measured all: 115312 / Scaling rejects: 3
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.988 / CC1/2: 0.779 / Rpim(I) all: 0.413 / Rrim(I) all: 1.072 / % possible all: 99.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIXdev_2775refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J0O

2j0o


Resolution: 2.55→38.122 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 30.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 1650 4.91 %Random selection
Rwork0.2021 ---
obs0.2054 33611 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 222 Å2 / Biso mean: 72.644 Å2 / Biso min: 21.07 Å2
Refinement stepCycle: final / Resolution: 2.55→38.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 0 17 3134
Biso mean---45.06 -
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023166
X-RAY DIFFRACTIONf_angle_d0.5364290
X-RAY DIFFRACTIONf_chiral_restr0.038492
X-RAY DIFFRACTIONf_plane_restr0.003557
X-RAY DIFFRACTIONf_dihedral_angle_d16.3771926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.6250.3611490.281126412790100
2.625-2.70970.36481230.28462686280999
2.7097-2.80650.33151470.294326582805100
2.8065-2.91890.40131220.285126592781100
2.9189-3.05170.37431620.282726652827100
3.0517-3.21250.30171350.237526662801100
3.2125-3.41360.33811340.236626692803100
3.4136-3.6770.28661460.200726352781100
3.677-4.04670.24321310.174327022833100
4.0467-4.63140.21821190.154626602779100
4.6314-5.83170.21981470.166826592806100
5.8317-38.12620.21571350.167126612796100
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)
1-0.00090.01720.0340.02170.0170.0116-0.1133-0.20390.0456-0.1175-0.54530.1828-0.03240.130600.28990.03710.13290.6746-0.0851-0.627-5.9128-21.1372-2.7435
20.01510.00280.01470.00140.0006-0.00590.0364-0.24220.334-0.0337-0.0185-0.03620.1082-0.185800.3033-0.05270.02080.5383-0.00860.2175-16.4913-27.2195-4.8514
3-0.0085-0.0109-0.0040.00050.0034-0.0036-0.0583-0.18470.2372-0.137-0.1-0.1051-0.0337-0.192900.2510.02640.01780.3991-0.12720.3342-15.9359-14.7176-7.8381
4-0.0024-0.00210.00280.036-0.0072-0.0003-0.2854-0.13490.17760.0607-0.4802-0.6725-0.1465-0.2563-0-0.43170.11230.90150.5058-0.3981-0.7495-12.4739-17.63720.5432
50.01150.06030.0768-0.0292-0.00420.00910.126-0.24710.1978-0.1509-0.32310.08860.2134-0.01-00.3023-0.00720.01630.3814-0.02810.2751-11.1265-25.4892-10.2888
60.12310.10580.1422-0.0099-0.00470.00060.2017-0.36280.30370.1872-0.08040.29810.0986-0.1114-00.5294-0.12970.02820.4439-0.05890.4675-8.614522.5132-26.4954
70.0867-0.18660.35280.13720.15740.1492-0.13880.11630.0759-0.150.06130.0764-0.02540.063800.31120.0365-0.05430.2686-0.02610.3727-5.419317.5247-35.7459
80.03460.11710.1680.05650.11550.0677-0.1429-0.0010.1086-0.19560.10550.12670.1496-0.1208-00.3118-0.027-0.07960.27280.02130.3699-18.4242-8.7412-37.7515
9-0.2620.1801-0.3432-0.05780.03270.26-0.06960.00280.04510.02780.05590.00030.0298-0.043-00.2519-0.0086-0.08120.1244-0.00970.3254-6.1384-0.6201-30.1768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 33 )B2 - 33
2X-RAY DIFFRACTION2chain 'B' and (resid 34 through 51 )B34 - 51
3X-RAY DIFFRACTION3chain 'B' and (resid 52 through 73 )B52 - 73
4X-RAY DIFFRACTION4chain 'B' and (resid 74 through 91 )B74 - 91
5X-RAY DIFFRACTION5chain 'B' and (resid 92 through 126 )B92 - 126
6X-RAY DIFFRACTION6chain 'A' and (resid 41 through 102 )A41 - 102
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 177 )A103 - 177
8X-RAY DIFFRACTION8chain 'A' and (resid 178 through 267 )A178 - 267
9X-RAY DIFFRACTION9chain 'A' and (resid 268 through 322 )A268 - 322

+
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