[English] 日本語
Yorodumi
- PDB-3s2q: The crystal structure of AT5g51720 (AT-NEET) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s2q
TitleThe crystal structure of AT5g51720 (AT-NEET)
ComponentsAT5g51720/MIO24_14
KeywordsMETAL BINDING PROTEIN / redox / Fe-S cluster
Function / homology
Function and homology information


leaf senescence / plastid / chloroplast stroma / reactive oxygen species metabolic process / chloroplast / regulation of autophagy / 2 iron, 2 sulfur cluster binding / mitochondrion / metal ion binding / cytosol
Similarity search - Function
CDGSH iron-sulfur domain, mitoNEET-type / CDGSH iron-sulfur domain-containing protein 1/2 / Iron-binding zinc finger CDGSH type / Iron-binding zinc finger, CDGSH type / MitoNEET, CDGSH iron-sulfur domain / CDGSH-type zinc finger. Function unknown. / Ribosomal Protein L9; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / CDGSH iron-sulfur domain-containing protein NEET
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLivnah, O. / Eisenberg-Domovich, Y. / Nechushtai, R.
CitationJournal: To be Published
Title: Arabidopsis thaliana ChloroNEET, a Member of the New NEET Family of Human Proteins, is Involved in Development, Senescence and Iron Metabolism.
Authors: Nechushtai, R. / Conlan, A.R. / Song, L. / Harir, Y. / Yogev, O. / Eisenberg-Domovich, Y. / Livnah, O. / Michaeli, D. / Rosen, R. / Ma, V. / Yuting, L. / Zuris, J.A. / Shulaev, V. / Paddock, ...Authors: Nechushtai, R. / Conlan, A.R. / Song, L. / Harir, Y. / Yogev, O. / Eisenberg-Domovich, Y. / Livnah, O. / Michaeli, D. / Rosen, R. / Ma, V. / Yuting, L. / Zuris, J.A. / Shulaev, V. / Paddock, M.L. / Cabantchik, Z.Y. / Jennings, P.A. / Mittler, R.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AT5g51720/MIO24_14
B: AT5g51720/MIO24_14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8886
Polymers18,4052
Non-polymers4824
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-110 kcal/mol
Surface area6740 Å2
MethodPISA
2
A: AT5g51720/MIO24_14
B: AT5g51720/MIO24_14
hetero molecules

A: AT5g51720/MIO24_14
B: AT5g51720/MIO24_14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,77512
Polymers36,8104
Non-polymers9658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area1250 Å2
ΔGint-84 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.548, 60.090, 66.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AT5g51720/MIO24_14 / Genomic DNA / chromosome 5 / P1 clone:MIO24


Mass: 9202.597 Da / Num. of mol.: 2 / Fragment: UNP residues 30-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g51720 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FLI7
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM ZnAc2 and 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2010
RadiationMonochromator: optical hutch / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.75→44.55 Å / Num. all: 16531 / Num. obs: 16531 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ew0

3ew0


Resolution: 1.75→44.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.059 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 836 5.1 %RANDOM
Rwork0.181 ---
obs0.183 15592 94.7 %-
all-15592 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---0.96 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 10 106 1120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221030
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9691388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2532544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94115186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.279156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021760
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2751.5644
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10721046
X-RAY DIFFRACTIONr_scbond_it3.1083386
X-RAY DIFFRACTIONr_scangle_it4.5894.5338
X-RAY DIFFRACTIONr_rigid_bond_restr1.50531030
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 51 -
Rwork0.247 1127 -
obs--93.27 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
1-12.21422.274-18.963
2-10.75610.641-20.836
31.2260.612-13.947
4-6.30118.6918-7.2253
5-4.7017.306-5.178
6-17.031617.37090.3374
7-14.97356.2984-8.607
8-23.87516.081-17.025
9-19.43419.775-17.868
10-10.3484.616-15.697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 53
2X-RAY DIFFRACTION2A54 - 62
3X-RAY DIFFRACTION3A63 - 67
4X-RAY DIFFRACTION4A68 - 101
5X-RAY DIFFRACTION5A102 - 106
6X-RAY DIFFRACTION6B44 - 53
7X-RAY DIFFRACTION7B54 - 88
8X-RAY DIFFRACTION8B89 - 94
9X-RAY DIFFRACTION9B95 - 101
10X-RAY DIFFRACTION10B102 - 106

+
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