[English] 日本語
Yorodumi
- PDB-5io8: Salmonella Typhimurium VirG-like (STV) protein at 2.19 Angstrom r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5io8
TitleSalmonella Typhimurium VirG-like (STV) protein at 2.19 Angstrom resolution solved by Iodine SAD.
ComponentsVirG-like protein
KeywordsUNKNOWN FUNCTION / LTxxQ motif / CpxP_like family / VirG-like protein
Function / homologyLTXXQ motif family protein / LTXXQ motif family protein / periplasmic space / IODIDE ION / PHOSPHATE ION / Probable secreted protein (SPI-6 associated)
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.192 Å
AuthorsPandey, N.K. / Ray, S. / Suar, M. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: To Be Published
Title: Salmonella Typhimurium VirG-like (STV) protein at at 2.19 Angstrom resolution by SAD.
Authors: Pandey, N.K. / Ray, S. / Suar, M. / Bhavesh, N.S.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VirG-like protein
B: VirG-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,57724
Polymers26,4002
Non-polymers2,17722
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-99 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.115, 60.277, 62.603
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUchain AAA8 - 1158 - 115
2ALAALAchain BBB8 - 1148 - 114

-
Components

#1: Protein VirG-like protein


Mass: 13200.012 Da / Num. of mol.: 2 / Fragment: UNP residues 24-135
Source method: isolated from a genetically manipulated source
Details: First four residues GSHM are from vector.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Strain: SL1344 / Gene: SL1344_RS01575 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3ND95*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.8 M Sodium phosphate monobasic monohydrate, potassium phosphate dibasic. pH=4.6-5.2. Crystal was soaked in 100mM Sodium Iodide for 5 minutes before flash freezing.
PH range: 4.6-5.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.771 Å
DetectorType: MAR CCD 225 / Detector: CCD / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 22529 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.058 / Net I/av σ(I): 45.26 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.19-2.236.90.403199
2.23-2.277.30.316199.5
2.27-2.317.30.293199.3
2.31-2.367.40.254199.6
2.36-2.417.40.203199.6
2.41-2.477.40.1781100
2.47-2.537.50.151199.6
2.53-2.67.50.1241100
2.6-2.677.50.119199.8
2.67-2.767.50.0941100
2.76-2.867.60.0851100
2.86-2.977.60.071100
2.97-3.117.60.0651100
3.11-3.277.60.0591100
3.27-3.487.70.0561100
3.48-3.747.70.0571100
3.74-4.127.60.0531100
4.12-4.727.80.0451100
4.72-5.947.80.041100
5.94-507.70.038199.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.192→31.302 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.88
Details: 1) UNMODELLED BLOB NEAR LEU 56 AND GLN 73 IN CHAIN A. 2) UNMODELLED BLOB NEAR LEU 56 AND GLN 73 IN CHAIN B. 3) UNMODELLED BLOB NEAR ALA 55 IN CHAIN A.
RfactorNum. reflection% reflection
Rfree0.2454 2259 10.04 %
Rwork0.2044 --
obs0.2085 22496 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.7 Å2 / Biso mean: 49.7085 Å2 / Biso min: 23.65 Å2
Refinement stepCycle: final / Resolution: 2.192→31.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 34 78 1683
Biso mean--85.76 47.61 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121611
X-RAY DIFFRACTIONf_angle_d1.1932198
X-RAY DIFFRACTIONf_chiral_restr0.054257
X-RAY DIFFRACTIONf_plane_restr0.009284
X-RAY DIFFRACTIONf_dihedral_angle_d14.931578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A879X-RAY DIFFRACTION11.477TORSIONAL
12B879X-RAY DIFFRACTION11.477TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.192-2.23960.28961460.24261262140897
2.2396-2.29170.31381320.23912361368100
2.2917-2.3490.24861650.21971260142599
2.349-2.41250.26531180.211812971415100
2.4125-2.48340.33361410.213812441385100
2.4834-2.56360.2811350.217112661401100
2.5636-2.65510.24031520.228412511403100
2.6551-2.76140.27071320.219712641396100
2.7614-2.8870.30141440.216612721416100
2.887-3.03910.24531420.22912741416100
3.0391-3.22930.25021350.215812831418100
3.2293-3.47830.26511510.207312551406100
3.4783-3.82780.2331300.197312671397100
3.8278-4.38040.21771480.167812781426100
4.3804-5.5140.20411540.187712471401100
5.514-31.30470.23651340.20712811415100
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)
10.3152-0.12390.440.14180.14491.6006-0.1735-0.7227-1.04690.415-0.04640.59370.0185-1.4447-0.01740.6219-0.08740.05540.80190.0920.571836.97275.21913.7217
21.1608-0.6922-0.33581.32810.08311.05440.50760.1814-0.4689-0.1610.1718-0.20460.4039-0.1240.02630.44780.0209-0.05820.26840.09520.401648.36424.245811.3318
35.42692.4595-6.04072.5132-4.47878.89111.3122-1.4612-0.30370.8658-1.0856-0.57670.73131.02110.04440.7192-0.0940.04220.549-0.01360.438457.929410.199630.4371
41.85040.3266-0.7620.96510.88461.42140.1258-0.35010.0310.02940.2776-0.16970.01190.74620.00160.32610.0952-0.0190.42230.00740.404750.989816.132529.8661
50.44390.3063-0.09330.7678-0.34490.1609-0.1457-1.12830.34640.40740.356-0.0830.0245-0.5923-00.5670.177-0.03910.9679-0.02550.473834.500515.57129.5138
62.8524-0.94990.76751.0974-0.6422.21370.0994-0.3409-0.25-0.09980.04460.08620.1593-0.0990.00010.35890.0029-0.05040.3124-0.05220.366234.178617.962947.2831
70.05890.04120.01930.10110.07110.56260.00660.06220.144-0.45570.02930.3354-1.6341-0.43110.01550.63020.180.09240.62360.21790.637843.998924.673714.9959
81.5999-0.2482-1.05671.0667-0.19740.84260.2404-0.28120.17080.0232-0.027-0.0594-0.56510.45860.00050.37720.0262-0.01090.3505-0.04310.434346.266722.135536.1116
90.14770.23280.0120.37330.06520.1426-0.13330.0377-0.6798-0.2660.2740.07860.24970.5824-0.00090.53510.1282-0.01320.64060.02450.494243.26987.862551.5149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 25 )A9 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 45 )A26 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 54 )A46 - 54
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 98 )A55 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 115 )A99 - 115
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 45 )B8 - 45
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 66 )B46 - 66
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 98 )B67 - 98
9X-RAY DIFFRACTION9chain 'B' and (resid 99 through 114 )B99 - 114

+
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://pdbjlvh1.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