[English] 日本語
Yorodumi
- PDB-1yvi: X-RAY STRUCTURE OF PUTATIVE HISTIDINE-CONTAINING PHOSPHOTRANSFER ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yvi
TitleX-RAY STRUCTURE OF PUTATIVE HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN FROM RICE, AK104879
Componentshistidine-containing phosphotransfer protein
KeywordsSIGNALING PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AK104879 / PHOSPHORELAY MEDIATOR / HP1 / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


positive regulation of cytokinin-activated signaling pathway / protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / nucleus / cytosol / cytoplasm
Similarity search - Function
Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine-containing phosphotransfer protein 2
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-RAY STRUCTURE OF PUTATIVE HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN FROM RICE, AK104879
Authors: Center for Eukaryotic Structural Genomics (CESG)
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 23, 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.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: histidine-containing phosphotransfer protein
B: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)33,5622
Polymers33,5622
Non-polymers00
Water5,747319
1
A: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)16,7811
Polymers16,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)16,7811
Polymers16,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.558, 100.558, 69.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASPAA3 - 353 - 35
21ALAALAASPASPBB3 - 353 - 35
12PROPROGLNGLNAA40 - 14240 - 142
22PROPROGLNGLNBB40 - 14240 - 142

NCS ensembles :
ID
1
2
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B)

-
Components

#1: Protein histidine-containing phosphotransfer protein


Mass: 16780.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: AK104879 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) P(LACI+RARE) / References: UniProt: Q6VAK4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.8 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 10 MG/ML PROTEIN, 1.0 M SODIUM CITRATE, 0.10 M PIPES, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 6.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97942
DetectorType: APS-1 / Detector: CCD / Date: Dec 16, 2004
Details: SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR: WATER COOLED
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionRedundancy: 8.4 % / Number: 24495 / Rmerge(I) obs: 0.105 / Χ2: 0.977 / D res high: 2 Å / D res low: 50 Å / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.935094.210.0390.9679.1
3.914.9397.710.0431.0818.4
3.423.9198.310.0551.119
3.113.4298.810.0720.9519.2
2.883.1198.710.0980.979.2
2.712.8899.510.1280.9719
2.582.7199.910.1741.0088.9
2.472.5899.910.1990.9748.7
2.372.4799.810.2390.9888.4
2.292.3799.610.270.9698.2
2.222.2999.810.3010.9828
2.152.2299.810.3350.9187.9
2.12.1599.710.3950.897.7
2.052.199.510.4870.9317.5
22.0599.510.5960.9037.2
ReflectionResolution: 2→37.77 Å / Num. obs: 24495 / % possible obs: 98.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.747
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 3.521 / % possible all: 99.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.515 / Cor.coef. Fo:Fc: 0.47
Highest resolutionLowest resolution
Rotation4 Å37.77 Å
Translation4 Å37.77 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0005refinement
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WN0

1wn0


Resolution: 2→37.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.518 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1249 5.1 %RANDOM
Rwork0.17246 ---
all0.175 ---
obs0.17525 23200 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 0 319 2502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.952972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0335272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97125.69116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90815405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8381512
X-RAY DIFFRACTIONr_chiral_restr0.1180.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21147
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21559
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.93941427
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5342199
X-RAY DIFFRACTIONr_scbond_it5.616875
X-RAY DIFFRACTIONr_scangle_it8.3298773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight position
11X-RAY DIFFRACTION0.60.5
22X-RAY DIFFRACTION2.032
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 86 -
Rwork0.192 1711 -
obs--99.39 %

+
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