[English] 日本語
Yorodumi
- PDB-4d6x: Crystal structure of the receiver domain of NtrX from Brucella abortus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d6x
TitleCrystal structure of the receiver domain of NtrX from Brucella abortus
ComponentsBACTERIAL REGULATORY, FIS FAMILY PROTEIN
KeywordsSIGNALING PROTEIN / BRUCELLOSIS / TWO-COMPONENT SYSTEM / RESPONSE REGULATOR / REC DOMAIN / MICROAEROBISIS
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 / Response regulator receiver domain ...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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / CbxX/CfqX superfamily:Chaperonin clpA/B:Response regulator receiver:Sigma-54 factor interaction domain:Helix-turn-helix, Fis
Similarity search - Component
Biological speciesBRUCELLA ABORTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKlinke, S. / Fernandez, I. / Carrica, M.C. / Otero, L.H. / Goldbaum, F.A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Snapshots of Conformational Changes Shed Light Into the Ntrx Receiver Domain Signal Transduction Mechanism
Authors: Fernandez, I. / Otero, L.H. / Klinke, S. / Carrica, M.C. / Goldbaum, F.A.
History
DepositionNov 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
B: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
C: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
D: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5387
Polymers65,3304
Non-polymers2073
Water1,49583
1
A: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4713
Polymers16,3331
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4022
Polymers16,3331
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BACTERIAL REGULATORY, FIS FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,3331
Polymers16,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BACTERIAL REGULATORY, FIS FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,3331
Polymers16,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 110.940, 119.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
BACTERIAL REGULATORY, FIS FAMILY PROTEIN / NTRX


Mass: 16332.590 Da / Num. of mol.: 4 / Fragment: RECEIVER DOMAIN, RESIDUES 1-126
Source method: isolated from a genetically manipulated source
Details: THE GENE SEQUENCE ENCODING THE RECEIVER DOMAIN C-TERMINAL REGION (RESIDUES 127-136) WAS OMITTED FROM THE FINAL CONSTRUCT DUE TO POTENTIAL CLASHES INTO THE CRYSTAL PACKING
Source: (gene. exp.) BRUCELLA ABORTUS (bacteria) / Strain: BRUCELLA MELITENSIS BIOVAR ABORTUS 2308 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q2YPW6
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.96 Å3/Da / Density % sol: 37.33 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 27% PEG 550 MME; 0.15 M MALIC ACID, PH 7.0; 0.1 M IMIDAZOLE, PH 6.9.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.11→40.64 Å / Num. obs: 30141 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 5.11 % / Biso Wilson estimate: 57.41 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.63
Reflection shellResolution: 2.11→2.24 Å / Redundancy: 5.28 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.98 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L5Z

1l5z


Resolution: 2.11→40.64 Å / Cor.coef. Fo:Fc: 0.9523 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 1507 5 %RANDOM
Rwork0.2134 ---
obs0.2137 30132 98.82 %-
Displacement parametersBiso mean: 74.48 Å2
Baniso -1Baniso -2Baniso -3
1--14.2838 Å20 Å20 Å2
2--9.264 Å20 Å2
3---5.0198 Å2
Refine analyzeLuzzati coordinate error obs: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2.11→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 15 83 3810
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013779HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085119HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1794SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it3779HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion508SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4511SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.18 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2257 144 5.01 %
Rwork0.2369 2732 -
all0.2363 2876 -
obs--98.82 %
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)
13.17551.76660.22298.30290.75571.634-0.0968-0.0036-0.5442-0.22-0.01190.00750.5442-0.23450.10870.1628-0.0459-0.1145-0.2963-0.0439-0.17024.656319.12219.9659
21.25480.5715-0.07732.4113-0.92068.2844-0.0415-0.18050.27920.54420.04530.0628-0.54420.4408-0.00380.06890.041-0.088-0.1973-0.0525-0.159711.912640.680138.0896
35.3983-1.66892.21328.3155-1.92844.6578-0.2587-0.45960.04720.52440.2081-0.0077-0.5442-0.36940.0506-0.04880.0334-0.0498-0.1945-0.0091-0.230914.435614.918551.4707
42.3658-0.0004-0.01645.03361.93163.67690.1926-0.2717-0.02740.4173-0.0243-0.02550.20320.1564-0.1684-0.1157-0.0348-0.0329-0.07410.0304-0.0836-7.3242-9.955550.233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

+
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