[English] 日本語
Yorodumi
- PDB-4ew5: C-terminal domain of inner membrane protein CigR from Salmonella ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ew5
TitleC-terminal domain of inner membrane protein CigR from Salmonella enterica.
ComponentsCigR Protein
KeywordsMEMBRANE PROTEIN / inner membrane protein / structural genomics / APC101781 / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP
Function / homologyinner membrane protein cigr / Nuclear Transport Factor 2; Chain: A, / Roll / membrane / Alpha Beta / CigR
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsOsipiuk, J. / Xu, X. / Cui, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Niemann, G.S. / Merkley, E.D. / Savchenko, A. ...Osipiuk, J. / Xu, X. / Cui, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Niemann, G.S. / Merkley, E.D. / Savchenko, A. / Adkins, J.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: C-terminal domain of inner membrane protein CigR from Salmonella enterica.
Authors: Osipiuk, J. / Xu, X. / Cui, H. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Niemann, G.S. / Merkley, E.D. / Savchenko, A. / Adkins, J.N. / Joachimiak, A.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CigR Protein
B: CigR Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9134
Polymers21,7892
Non-polymers1242
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-8 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.870, 54.811, 73.992
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CigR Protein / Putative inner membrane protein


Mass: 10894.444 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: cigR, STM3762 / Plasmid: pET21b-L No TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z621
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes buffer, 2% PEG-400, 2M Ammonium sulphate. Full length protein was crystallized in presence of V8 protease., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 19, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.87→41.4 Å / Num. all: 17270 / Num. obs: 17270 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.107 / Χ2: 2.551 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.88-1.915.60.8112.28601.051100
1.91-1.956.20.5958391.078100
1.95-1.9870.6038411.091100
1.98-2.037.10.4818571.112100
2.03-2.077.10.4138301.251100
2.07-2.127.10.368631.35100
2.12-2.177.10.3018301.453100
2.17-2.237.10.2948581.506100
2.23-2.297.10.2298671.814100
2.29-2.377.10.2068451.816100
2.37-2.457.10.198411.823100
2.45-2.557.10.1648752.081100
2.55-2.6770.1428542.258100
2.67-2.817.10.1298552.38699.9
2.81-2.9870.1098702.915100
2.98-3.216.90.0968643.658100
3.21-3.546.70.0878804.375100
3.54-4.056.60.0788815.225100
4.05-5.16.40.0728985.658100
5.1-506.30.0729626.95199.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→41.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.798 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 871 5.1 %RANDOM
Rwork0.1757 ---
all0.1783 17222 --
obs0.1783 17222 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.97 Å2 / Biso mean: 31.4572 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---0.9 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.87→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 8 145 1636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021573
X-RAY DIFFRACTIONr_bond_other_d0.0010.021075
X-RAY DIFFRACTIONr_angle_refined_deg1.832.0052154
X-RAY DIFFRACTIONr_angle_other_deg1.03632663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18124.03852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11515258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.231157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02283
LS refinement shellResolution: 1.872→1.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 55 -
Rwork0.243 1014 -
all-1069 -
obs-1069 93.28 %
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)
11.4698-0.76331.11280.7012-0.13791.486-0.05070.10050.18-0.1061-0.0609-0.1021-0.22490.04780.11160.0646-0.0113-0.00150.03830.02720.081817.3206-5.266831.3267
20.1367-0.2170.05470.86820.20750.65130.0453-0.0451-0.0268-0.1463-0.05750.0621-0.0071-0.08460.01220.07140.0008-0.00790.04750.01030.08763.818-15.029313.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 161
2X-RAY DIFFRACTION2B64 - 160

+
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