[English] 日本語
Yorodumi
- PDB-6ph2: Complete LOV domain from the LOV-HK sensory protein from Brucella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ph2
TitleComplete LOV domain from the LOV-HK sensory protein from Brucella abortus (mutant C69S, construct 15-155)
ComponentsBlue-light-activated histidine kinase
KeywordsTRANSFERASE / PAS SUPERFAMILY / BLUE-LIGHT PHOTORECEPTOR / FMN BINDING
Function / homology
Function and homology information


protein histidine kinase activity / histidine kinase / photoreceptor activity / ATP binding
Similarity search - Function
Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / PAS fold-3 / PAS fold / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / PAS fold-3 / PAS fold / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Blue-light-activated histidine kinase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsRinaldi, J. / Otero, L.H. / Fernandez, I. / Goldbaum, F.A. / Shin, H. / Yang, X. / Klinke, S.
Funding support Argentina, 3items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2011-2672 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2014-0959 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2016-1618 Argentina
CitationJournal: Mbio / Year: 2021
Title: Dimer Asymmetry and Light Activation Mechanism in Brucella Blue-Light Sensor Histidine Kinase.
Authors: Rinaldi, J. / Fernandez, I. / Shin, H. / Sycz, G. / Gunawardana, S. / Kumarapperuma, I. / Paz, J.M. / Otero, L.H. / Cerutti, M.L. / Zorreguieta, A. / Ren, Z. / Klinke, S. / Yang, X. / Goldbaum, F.A.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Blue-light-activated histidine kinase
B: Blue-light-activated histidine kinase
C: Blue-light-activated histidine kinase
D: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8348
Polymers67,0084
Non-polymers1,8254
Water1,29772
1
A: Blue-light-activated histidine kinase
B: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4174
Polymers33,5042
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-29 kcal/mol
Surface area12510 Å2
MethodPISA
2
C: Blue-light-activated histidine kinase
D: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4174
Polymers33,5042
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-29 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.270, 95.860, 107.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA19 - 1406 - 127
21ALAALABB19 - 1406 - 127
12ALAALAAA19 - 1406 - 127
22ALAALACC19 - 1406 - 127
13GLNGLNAA18 - 1405 - 127
23GLNGLNDD18 - 1405 - 127
14ALAALABB19 - 1406 - 127
24ALAALACC19 - 1406 - 127
15ALAALABB19 - 1406 - 127
25ALAALADD19 - 1406 - 127
16ALAALACC19 - 1406 - 127
26ALAALADD19 - 1406 - 127

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Blue-light-activated histidine kinase / BM-LOV-histidine kinase / BM-LOV-HK


Mass: 16752.086 Da / Num. of mol.: 4 / Mutation: C69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0679 / Plasmid: pET-24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q8YC53, histidine kinase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 15% (w/v) PEG 3350 + 0.1 M sodium citrate, pH 5.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2016 / Details: KIRKPATRICK-BAEZ PAIR OF BIMORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.34→48.63 Å / Num. obs: 29308 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.154 / Net I/σ(I): 11.6
Reflection shellResolution: 2.34→2.49 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4523 / CC1/2: 0.506 / Rrim(I) all: 0.624 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T50

3t50


Resolution: 2.34→48.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.903 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.26071 1466 5 %RANDOM
Rwork0.22743 ---
obs0.22909 27840 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.838 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20 Å2
2---0.28 Å2-0 Å2
3----2.68 Å2
Refinement stepCycle: 1 / Resolution: 2.34→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 124 72 4096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0154132
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173647
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.7595639
X-RAY DIFFRACTIONr_angle_other_deg0.4371.7158549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.80419.398166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98715567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3641528
X-RAY DIFFRACTIONr_chiral_restr0.0590.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
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_it3.093.8951980
X-RAY DIFFRACTIONr_mcbond_other3.0893.8981981
X-RAY DIFFRACTIONr_mcangle_it4.9875.822468
X-RAY DIFFRACTIONr_mcangle_other4.9865.8232469
X-RAY DIFFRACTIONr_scbond_it3.9284.3022152
X-RAY DIFFRACTIONr_scbond_other3.934.3032149
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2966.2353172
X-RAY DIFFRACTIONr_long_range_B_refined8.48145.9044172
X-RAY DIFFRACTIONr_long_range_B_other8.48245.9024171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A37520.08
12B37520.08
21A37490.07
22C37490.07
31A37950.06
32D37950.06
41B37730.08
42C37730.08
51B37750.07
52D37750.07
61C37300.07
62D37300.07
LS refinement shellResolution: 2.343→2.404 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 100 -
Rwork0.412 1889 -
obs--92.81 %

+
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