[English] 日本語
Yorodumi
- PDB-5m7o: Crystal structure of NtrX from Brucella abortus processed with th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m7o
TitleCrystal structure of NtrX from Brucella abortus processed with the CrystalDirect automated mounting and cryo-cooling technology
ComponentsNitrogen assimilation regulatory protein
KeywordsSIGNALING PROTEIN / CRYSTALDIRECT / BRUCELLOSIS / TWO-COMPONENT SYSTEM
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 ...Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nitrogen assimilation regulatory protein
Similarity search - Component
Biological speciesBrucella abortus str. 2308 A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCornaciu, I. / Fernandez, I. / Hoffmann, G. / Carrica, M.C. / Goldbaum, F.A. / Marquez, J.A.
Funding support Argentina, France, 3items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y TecnologicaPICT-2013-1629 Argentina
BioStruct-X283570 France
iNEXT653706 France
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Three-Dimensional Structure of Full-Length NtrX, an Unusual Member of the NtrC Family of Response Regulators.
Authors: Fernandez, I. / Cornaciu, I. / Carrica, M.D. / Uchikawa, E. / Hoffmann, G. / Sieira, R. / Marquez, J.A. / Goldbaum, F.A.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrogen assimilation regulatory protein
B: Nitrogen assimilation regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6104
Polymers100,5612
Non-polymers492
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-51 kcal/mol
Surface area39290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.778, 191.228, 111.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Nitrogen assimilation regulatory protein


Mass: 50280.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein chain not built between residues 137-142, flexible region not clearly visible in the electron density. Also the initial G and the final V are not seen in the electron density.
Source: (gene. exp.) Brucella abortus str. 2308 A (bacteria)
Gene: BAAA_2000042 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: C4IRH0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.36 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→50.02 Å / Num. obs: 67838 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.07 / Rrim(I) all: 0.167 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.226 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→50.02 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.245 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26896 3401 5 %RANDOM
Rwork0.22736 ---
obs0.22951 64403 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.365 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å2-0 Å20 Å2
2---0.93 Å2-0 Å2
3---3.45 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 2 122 6946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196915
X-RAY DIFFRACTIONr_bond_other_d0.0060.026868
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9769338
X-RAY DIFFRACTIONr_angle_other_deg0.981315718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30123.229319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.385151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7131580
X-RAY DIFFRACTIONr_chiral_restr0.0820.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217819
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021533
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8065.6463531
X-RAY DIFFRACTIONr_mcbond_other3.8055.6453530
X-RAY DIFFRACTIONr_mcangle_it5.8748.4444405
X-RAY DIFFRACTIONr_mcangle_other5.8748.4454406
X-RAY DIFFRACTIONr_scbond_it4.1896.1043384
X-RAY DIFFRACTIONr_scbond_other4.1886.1053385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7798.9664934
X-RAY DIFFRACTIONr_long_range_B_refined9.30666.5897442
X-RAY DIFFRACTIONr_long_range_B_other9.3166.6047438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 247 -
Rwork0.415 4670 -
obs--99.27 %

+
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