[English] 日本語
Yorodumi
- PDB-3o3t: Crystal Structure Analysis of M32A mutant of human CLIC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o3t
TitleCrystal Structure Analysis of M32A mutant of human CLIC1
ComponentsChloride intracellular channel protein 1Chloride channel
KeywordsTRANSPORT PROTEIN / CLIC / Glutathione Transferase / thioredoxin / ion channel / domain interface
Function / homology
Function and homology information


chloride transport / chloride channel activity / chloride channel complex / brush border / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / nuclear membrane / blood microparticle ...chloride transport / chloride channel activity / chloride channel complex / brush border / positive regulation of osteoblast differentiation / regulation of mitochondrial membrane potential / platelet aggregation / nuclear envelope / nuclear membrane / blood microparticle / vesicle / cadherin binding / perinuclear region of cytoplasm / endoplasmic reticulum / signal transduction / mitochondrion / extracellular space / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Chloride intracellular channel protein 1 / Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Chloride intracellular channel protein 1 / Intracellular chloride channel / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chloride intracellular channel protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsFanucchi, S. / Achilonu, I.A. / Adamson, R.J. / Fernandes, M.A. / Stoychev, S. / Dirr, H.W.
CitationJournal: To be Published
Title: Crystal Structure Analysis of M32A mutant of human CLIC1
Authors: Fanucchi, S. / Stoychev, S.H. / Achilonu, I.A. / Adamson, R. / Fernandes, M.A. / Dirr, H.W.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
SupersessionSep 8, 2010ID: 3MA4
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Chloride intracellular channel protein 1


Theoretical massNumber of molelcules
Total (without water)26,8931
Polymers26,8931
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.360, 63.985, 82.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Chloride intracellular channel protein 1 / Chloride channel / Nuclear chloride ion channel 27 / NCC27 / Chloride channel ABP / Regulatory nuclear chloride ion ...Nuclear chloride ion channel 27 / NCC27 / Chloride channel ABP / Regulatory nuclear chloride ion channel protein / hRNCC


Mass: 26892.566 Da / Num. of mol.: 1 / Mutation: M32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIC1, G6, NCC27 / Plasmid: pGex-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00299
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% (w/v) PEG 3350, 0.1M Tris-HCl, 0.2M sodium acetate pH 7.5, 0.02% azide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 5, 2009 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→50.63 Å / Num. obs: 25911 / % possible obs: 98.59 % / Redundancy: 5.24 % / Rsym value: 0.148 / Net I/σ(I): 166.319
Reflection shell
Resolution (Å)Rsym value
1.59-1.6470.657
1.647-1.7130.607
1.713-1.7910.505
1.791-1.8850.361
1.885-2.0030.234
2.003-2.1580.181
2.158-2.3750.179
2.375-2.7190.178
2.719-3.4260.155
3.426-50.630.115

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.48 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å50.63 Å
Translation2.5 Å50.63 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 30027
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.59-10028.40.722508
5.16-6.5930.10.85505
4.44-5.1627.60.873556
3.95-4.44250.887613
3.6-3.9521.70.869685
3.32-3.626.30.854729
3.1-3.3226.10.846788
2.92-3.129.10.825841
2.77-2.9228.10.838883
2.64-2.7728.20.847918
2.52-2.6426.30.86977
2.42-2.5227.70.8611005
2.33-2.4228.70.8531046
2.25-2.33270.8591072
2.18-2.2527.40.8561120
2.12-2.18290.8681144
2.06-2.12280.8521188
2-2.0629.90.8421220
1.95-232.40.821234
1.9-1.9532.50.8271284
1.86-1.937.10.7961305
1.82-1.8634.90.8181337
1.78-1.8234.80.8011339
1.74-1.7837.80.7631403
1.71-1.7438.90.7451419
1.68-1.7140.50.7521443
1.65-1.6842.70.7191456
1.6-1.6546.60.6352009

-
Processing

Software
NameVersionClassificationNB
SAINTV7.34Adata scaling
PHASER2.1.4phasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50.63 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.2208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7754 / SU B: 7.608 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1395 / SU Rfree: 0.1349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1293 5.1 %RANDOM
Rwork0.2292 ---
obs0.2313 25462 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.89 Å2 / Biso mean: 17.4453 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 150 2001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221889
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9832563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33525.11686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31815326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.648159
X-RAY DIFFRACTIONr_chiral_restr0.1370.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211425
X-RAY DIFFRACTIONr_mcbond_it0.3351.51180
X-RAY DIFFRACTIONr_mcangle_it0.80921906
X-RAY DIFFRACTIONr_scbond_it2.2323709
X-RAY DIFFRACTIONr_scangle_it3.5944.5657
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 93 -
Rwork0.334 1758 -
all-1851 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.232 Å / Origin y: 1.802 Å / Origin z: 16.3 Å
111213212223313233
T0.1321 Å2-0.0089 Å2-0.0045 Å2-0.1936 Å20.0088 Å2--0.0213 Å2
L1.2836 °2-0.2392 °20.0604 °2-0.5134 °20.0338 °2--1.1706 °2
S-0.0094 Å °0.017 Å °0.0371 Å °-0.0195 Å °0.0038 Å °-0.0116 Å °-0.0139 Å °0.0401 Å °0.0056 Å °

+
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