[English] 日本語
Yorodumi
- PDB-6kew: Crystal structure of oxidized phosphoribulokinase from Arabidopsi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kew
TitleCrystal structure of oxidized phosphoribulokinase from Arabidopsis thaliana
ComponentsPhosphoribulokinase
KeywordsTRANSFERASE / phosphoribulokinase oxidized
Function / homology
Function and homology information


phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / thylakoid / chloroplast stroma / chloroplast thylakoid membrane ...phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / stromule / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / thylakoid / chloroplast stroma / chloroplast thylakoid membrane / response to cold / chloroplast / disordered domain specific binding / phosphorylation / protein homodimerization activity / ATP binding / nucleus
Similarity search - Function
Phosphoribulokinase signature. / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phosphoribulokinase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsYu, A. / Xie, Y. / Li, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770778 China
CitationJournal: Plant Cell / Year: 2020
Title: Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle.
Authors: Yu, A. / Xie, Y. / Pan, X. / Zhang, H. / Cao, P. / Su, X. / Chang, W. / Li, M.
History
DepositionJul 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoribulokinase
B: Phosphoribulokinase


Theoretical massNumber of molelcules
Total (without water)81,0042
Polymers81,0042
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-7 kcal/mol
Surface area30530 Å2
Unit cell
Length a, b, c (Å)80.784, 50.315, 194.783
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

21A-492-

HOH

-
Components

#1: Protein Phosphoribulokinase / / PRKase / Phosphopentokinase


Mass: 40501.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g32060, T12O21.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25697, phosphoribulokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 4% v/v Tacsimate pH5.0, 12% w/v polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 23859 / % possible obs: 95.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Χ2: 0.881 / Net I/σ(I): 18.1
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 1703 / CC1/2: 0.978 / Rpim(I) all: 0.232 / Rrim(I) all: 0.601 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KEX

6kex


Resolution: 2.29→42.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2593 --
Rwork0.2408 --
obs-23781 79.37 %
Displacement parametersBiso mean: 44.16 Å2
Refinement stepCycle: LAST / Resolution: 2.29→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 0 174 5605
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)
12.04080.8466-1.06721.266-0.6934.5933-0.1422-0.08230.22040.10.26430.4862-0.4088-0.773-0.11240.23620.1432-0.00030.58190.06610.34-20.302317.439936.7304
22.73610.1482-0.3091.1757-0.16972.0452-0.0649-0.06610.52260.19190.0142-0.0186-0.3487-0.21430.03080.21630.0748-0.0510.17280.01530.2904-12.303126.816822.0378
33.08240.5550.32911.0543-0.51434.089-0.0445-0.2069-0.0661-0.0213-0.0087-0.0310.2457-0.55770.04080.1663-0.0095-0.00740.1094-0.03870.2258-10.207412.774910.5319
42.8321-1.0001-1.34581.60070.56783.3164-0.11050.1826-0.0784-0.54320.0286-0.83440.73291.07120.06790.48740.12150.08990.93060.07850.473-22.5895-0.056170.4439
52.37110.0121-1.90211.7522-0.55153.5576-0.14620.1757-0.2268-0.3388-0.2051-0.1510.48950.30440.25380.35160.10790.03290.46780.0280.2183-25.02046.117659.455
63.37670.4667-1.0591.399-0.12223.64150.2305-0.09180.83690.2958-0.0633-0.3518-0.34950.6239-0.22430.3226-0.01260.01340.3797-0.01510.4851-22.57823.852974.6025
72.6918-0.0189-1.49791.8214-0.34693.5061-0.08360.0442-0.00740.1180.03320.02910.13870.19660.09070.20560.01170.00770.28160.02860.1363-35.5819.87880.7639
82.8046-0.2154-0.78332.3035-0.17723.8855-0.2539-0.0952-0.26840.0072-0.0695-0.11560.70080.85450.27770.34460.15260.08110.58660.08460.2573-33.20510.218286.7859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 127 )A5 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 232 )A128 - 232
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 346 )A233 - 346
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 40 )B5 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 149 )B41 - 149
6X-RAY DIFFRACTION6chain 'B' and (resid 150 through 186 )B150 - 186
7X-RAY DIFFRACTION7chain 'B' and (resid 187 through 232 )B187 - 232
8X-RAY DIFFRACTION8chain 'B' and (resid 233 through 347 )B233 - 347

+
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