[English] 日本語
Yorodumi
- PDB-5f64: Putative positive transcription regulator (sensor EvgS) from Shig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f64
TitlePutative positive transcription regulator (sensor EvgS) from Shigella flexneri
ComponentsPositive transcription regulator EvgA
Keywordstranscription regulator / sensor / EvgS / structural genomics / IDP00102 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-binding transcriptional activator EvgA
Similarity search - Component
Biological speciesShigella flexneri 2a str. 2457T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsNocek, B. / Osipiuk, J. / Mulligan, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: to be published
Title: Putative positive transcription regulator (sensor EvgS) from Shigella flexneri.
Authors: Nocek, B. / Osipiuk, J. / Mulligan, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
A: Positive transcription regulator EvgA
B: Positive transcription regulator EvgA
C: Positive transcription regulator EvgA
D: Positive transcription regulator EvgA


Theoretical massNumber of molelcules
Total (without water)91,9624
Polymers91,9624
Non-polymers00
Water1,928107
1
A: Positive transcription regulator EvgA
D: Positive transcription regulator EvgA


Theoretical massNumber of molelcules
Total (without water)45,9812
Polymers45,9812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area18750 Å2
MethodPISA
2
B: Positive transcription regulator EvgA
C: Positive transcription regulator EvgA


Theoretical massNumber of molelcules
Total (without water)45,9812
Polymers45,9812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-15 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.485, 110.867, 110.769
Angle α, β, γ (deg.)90.000, 126.740, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Positive transcription regulator EvgA


Mass: 22990.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria)
Strain: 2457T / Gene: evgA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACZ7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 4.51 Å3/Da / Density % sol: 72.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M tri-sodium citrate, 0.1 M TRIS buffer, 15% PEG-400

-
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: Jun 15, 2009
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: 2.7→40 Å / Num. all: 43850 / Num. obs: 43850 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.049 / Rrim(I) all: 0.095 / Χ2: 0.968 / Net I/av σ(I): 16.962 / Net I/σ(I): 9.8 / Num. measured all: 164723
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.50.831.720600.7930.5120.9780.96495
2.75-2.83.60.8621420.7090.5251.0090.9697.2
2.8-2.853.70.72822060.7130.4450.8550.9899.3
2.85-2.913.70.55521750.8680.3360.650.95199.7
2.91-2.973.80.56921880.8470.3390.6640.983100
2.97-3.043.80.45422300.9050.2690.5280.974100
3.04-3.123.80.34521880.9420.2050.4020.961100
3.12-3.23.80.2921960.9530.1710.3370.974100
3.2-3.33.80.21521970.9650.1280.250.979100
3.3-3.43.80.17721830.9760.1050.2060.989100
3.4-3.523.80.12822100.9880.0760.1480.935100
3.52-3.663.80.10222010.9920.0610.1190.987100
3.66-3.833.80.0822060.9940.0480.0930.983100
3.83-4.033.80.07822040.9920.0460.0911.09100
4.03-4.283.80.0722020.9920.0420.0821.236100
4.28-4.623.80.06422320.9930.0380.0751.373100
4.62-5.083.80.05422050.9950.0320.0631.08100
5.08-5.813.70.04522400.9970.0270.0530.771100
5.81-7.313.70.03622260.9970.0220.0420.597100
7.31-403.60.0321590.9980.0190.0360.53795

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F6C

3f6c


Resolution: 2.71→39.2 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 18.81 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 1928 5.1 %RANDOM
Rwork0.1831 ---
obs0.1851 36035 85.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.61 Å2 / Biso mean: 48.234 Å2 / Biso min: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å2-0.12 Å2
2---0.32 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.71→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 0 107 6471
Biso mean---34.95 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196467
X-RAY DIFFRACTIONr_bond_other_d0.0010.026439
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9688707
X-RAY DIFFRACTIONr_angle_other_deg0.784314816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.89125.315286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.761151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5011532
X-RAY DIFFRACTIONr_chiral_restr0.0750.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021403
X-RAY DIFFRACTIONr_mcbond_it2.2753.3953267
X-RAY DIFFRACTIONr_mcbond_other2.2753.3953266
X-RAY DIFFRACTIONr_mcangle_it3.7445.0844079
LS refinement shellResolution: 2.709→2.779 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 76 -
Rwork0.269 1638 -
all-1714 -
obs--52.75 %
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)
10.0211-0.04840.20060.8025-0.00652.2958-0.0021-0.0122-0.0026-0.1212-0.13610.222-0.2525-0.19920.13820.11490.0186-0.05670.0763-0.04520.0706-0.227523.658131.5525
20.5517-0.36070.01330.8387-0.23331.1022-0.0718-0.0257-0.1040.0039-0.08060.0292-0.02740.01510.15240.1254-0.0656-0.00140.07520.01390.04417.5128.519353.7888
33.0993-0.2398-1.20010.07480.30611.3275-0.043-0.4582-0.1875-0.02970.03430.0171-0.12710.21760.00870.1358-0.01220.06220.07150.0280.09642.25113.751658.9522
40.81160.05630.61440.06830.23861.1219-0.06260.0320.06410.018-0.02780.0073-0.0537-0.02520.09040.1506-0.001-0.06830.1222-0.0060.03531.19730.111214.4475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 203
2X-RAY DIFFRACTION2B0 - 203
3X-RAY DIFFRACTION3C0 - 203
4X-RAY DIFFRACTION4D0 - 203

+
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