[English] 日本語
Yorodumi
- PDB-8pbw: Histidine-containing phosphotransfer protein from Chaetomium ther... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pbw
TitleHistidine-containing phosphotransfer protein from Chaetomium thermophilum
ComponentsHPt domain-containing protein
KeywordsTRANSFERASE / Histidine-containing phosphotransferase / Fungal / Phosphorelay
Function / homology
Function and homology information


protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / nucleus / cytoplasm
Similarity search - Function
Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily
Similarity search - Domain/homology
HPt domain-containing protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsParedes-Martinez, F. / Casino, P.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-110630GB-I00 Spain
CitationJournal: Commun Biol / Year: 2024
Title: Structural and functional insights underlying recognition of histidine phosphotransfer protein in fungal phosphorelay systems.
Authors: Paredes-Martinez, F. / Eixeres, L. / Zamora-Caballero, S. / Casino, P.
History
DepositionJun 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: HPt domain-containing protein
A: HPt domain-containing protein
C: HPt domain-containing protein
D: HPt domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8777
Polymers75,6914
Non-polymers1863
Water1,54986
1
B: HPt domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9852
Polymers18,9231
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HPt domain-containing protein


Theoretical massNumber of molelcules
Total (without water)18,9231
Polymers18,9231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HPt domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9852
Polymers18,9231
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HPt domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9852
Polymers18,9231
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.885, 149.334, 65.365
Angle α, β, γ (deg.)90.00, 101.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

-
Components

#1: Protein
HPt domain-containing protein


Mass: 18922.744 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0013690 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): SHuffle-T7 / References: UniProt: G0S1I2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.5 M Sodium Citrate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→74.78 Å / Num. obs: 35171 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Χ2: 0.84 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.57 / Num. measured all: 22834 / Num. unique obs: 3660 / CC1/2: 0.87 / Rpim(I) all: 0.248 / Rrim(I) all: 0.623 / Χ2: 0.82 / Net I/σ(I) obs: 2.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→74.78 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.842 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 1784 5.1 %RANDOM
Rwork0.22929 ---
obs0.23115 33381 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-1.63 Å2
2---1 Å2-0 Å2
3---1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.4→74.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 12 86 4111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124111
X-RAY DIFFRACTIONr_bond_other_d0.0050.0163798
X-RAY DIFFRACTIONr_angle_refined_deg0.9651.6395534
X-RAY DIFFRACTIONr_angle_other_deg0.371.5778784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7465522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.59512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75910689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0460.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02899
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_it2.7395.1922103
X-RAY DIFFRACTIONr_mcbond_other2.7395.1922103
X-RAY DIFFRACTIONr_mcangle_it4.3449.3242620
X-RAY DIFFRACTIONr_mcangle_other4.3439.3252621
X-RAY DIFFRACTIONr_scbond_it3.1235.4912008
X-RAY DIFFRACTIONr_scbond_other3.1225.4912009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2399.9782915
X-RAY DIFFRACTIONr_long_range_B_refined6.80548.344555
X-RAY DIFFRACTIONr_long_range_B_other6.80448.364543
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1225loose positional0.565
11B1225loose positional0.575
11C1225loose positional0.525
11D1225loose positional0.525
22A354loose positional0.415
22B354loose positional0.395
22C354loose positional0.455
22D354loose positional0.475
11A1225loose thermal3.9210
11B1225loose thermal4.1710
11C1225loose thermal6.9510
11D1225loose thermal6.3610
22A354loose thermal3.7210
22B354loose thermal5.8710
22C354loose thermal7.4710
22D354loose thermal8.110
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 112 -
Rwork0.294 2485 -
obs--99.54 %

+
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