[English] 日本語
Yorodumi
- PDB-4gqw: Crystal structure of CBS-pair protein, CBSX1 (loop deletion) from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gqw
TitleCrystal structure of CBS-pair protein, CBSX1 (loop deletion) from Arabidopsis thaliana
ComponentsCBS domain-containing protein CBSX1, chloroplastic
KeywordsPROTEIN BINDING / CBS domain / Thioredoxin / Chloroplast / plant
Function / homology
Function and homology information


cell redox homeostasis / chloroplast
Similarity search - Function
CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
CBS domain-containing protein CBSX1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsJeong, B.-C. / Song, H.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structure of CBSX1 (loop deletion)
Authors: Jeong, B.C. / Park, S.H. / Yoo, K.S. / Shin, J.S. / Song, H.K.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CBS domain-containing protein CBSX1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)16,6901
Polymers16,6901
Non-polymers00
Water54030
1
A: CBS domain-containing protein CBSX1, chloroplastic

A: CBS domain-containing protein CBSX1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)33,3802
Polymers33,3802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3120 Å2
ΔGint-17 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.818, 55.818, 83.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein CBS domain-containing protein CBSX1, chloroplastic / CBS domain-containing protein 2 / AtCDCP2 / Protein LOSS OF THE TIMING OF ET AND JA BIOSYNTHESIS 2 / AtLEJ2


Mass: 16690.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AP22.61, At4g36910, C7A10.450, CBSX1, CDCP2 / Plasmid: pET-GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O23193
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6, 2.0M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: double-crystal Si(111) liquid-nitrogen-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 9801 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.9 % / Rsym value: 0.044 / Net I/σ(I): 64.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→31.489 Å / SU ML: 0.29 / σ(F): 1.16 / Phase error: 37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.311 752 9.9 %
Rwork0.2578 --
obs0.2632 7598 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→31.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 0 30 1050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041039
X-RAY DIFFRACTIONf_angle_d0.7281411
X-RAY DIFFRACTIONf_dihedral_angle_d13.516382
X-RAY DIFFRACTIONf_chiral_restr0.046177
X-RAY DIFFRACTIONf_plane_restr0.003175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2005-2.37040.39871390.34821248X-RAY DIFFRACTION89
2.3704-2.60880.41991450.32331314X-RAY DIFFRACTION93
2.6088-2.9860.37491460.31191358X-RAY DIFFRACTION96
2.986-3.76110.34451570.25141436X-RAY DIFFRACTION99
3.7611-31.49180.24811650.22281490X-RAY DIFFRACTION99
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)
10.23351.95041.27721.52860.38811.0966-0.4153-0.14180.0644-0.16340.5443-0.4235-0.88421.795500.8665-0.10070.10841.2719-0.05220.81620.506312.3344-11.4881
21.68390.01231.22561.8872-0.55361.0773-0.73230.3395-0.1491-0.3710.02070.75810.53141.23870.47370.9371-0.14680.05250.8894-0.00830.908510.0628.7402-25.1176
30.3509-0.46980.2112-0.0849-0.30220.5169-0.54980.15070.4083-0.57720.22140.3542-1.3935-0.4044-0.41211.1635-0.2088-0.1090.99730.0320.924210.066817.384-20.7382
41.6674-0.199-0.37361.19670.5841.58440.02820.0341-0.28730.1150.2596-0.0785-0.09150.9891-0.00020.78670.0326-0.01691.0348-0.02620.750713.92497.2671-0.1321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 73:119 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 120:160 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 161:180 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 181:227 )

+
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