[English] 日本語
Yorodumi
- PDB-1ut4: Structure of the conserved domain of ANAC, a member of the NAC fa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ut4
TitleStructure of the conserved domain of ANAC, a member of the NAC family of transcription factors
ComponentsNO APICAL MERISTEM PROTEIN
KeywordsTRANSCRIPTION REGULATION / TRANSCRIPTION / TRANSCRIPTION FACTOR / DNA BINDING / ABSCISIC ACID RESPONSE / ARABIDOPSIS THALIANA / NAC DOMAIN
Function / homology
Function and homology information


response to water deprivation / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
NAC domain / NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
NAC domain-containing protein 19
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsErnst, H.A. / Olsen, A.N. / Skriver, K. / Larsen, S. / Lo Leggio, L.
Citation
Journal: Embo Rep. / Year: 2004
Title: Structure of the Conserved Domain of Anac, a Member of the Nac Family of Transcription Factors
Authors: Ernst, H.A. / Olsen, A.N. / Skriver, K. / Larsen, S. / Lo Leggio, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Preliminary Crystallographic Analysis of the Nac Domain of Anac, a Member of the Plant-Specific Nac Transcription Factor Family
Authors: Olsen, A. / Ernst, H. / Lo Leggio, L. / Johansson, E. / Larsen, S. / Skriver, K.
History
DepositionDec 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NO APICAL MERISTEM PROTEIN
B: NO APICAL MERISTEM PROTEIN


Theoretical massNumber of molelcules
Total (without water)39,5612
Polymers39,5612
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.953, 75.224, 80.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHE4AA16 - 2019 - 23
21PROPROPHEPHE4BB16 - 2019 - 23
12TYRTYRASPASP1AA21 - 2424 - 27
22TYRTYRASPASP1BB21 - 2424 - 27
13GLUGLUGLUGLU3AA2528
23GLUGLUGLUGLU3BB2528
14GLUGLULEULEU1AA26 - 3229 - 35
24GLUGLULEULEU1BB26 - 3229 - 35
15ARGARGLYSLYS6AA34 - 3537 - 38
25ARGARGLYSLYS6BB34 - 3537 - 38
16ILEILEILEILE3AA4952
26ILEILEILEILE3BB4952
17ASPASPASPASP1AA5053
27ASPASPASPASP1BB5053
18LEULEULEULEU2AA5154
28LEULEULEULEU2BB5154
19TYRTYRTYRTYR1AA5255
29TYRTYRTYRTYR1BB5255
110LYSLYSLYSLYS3AA5356
210LYSLYSLYSLYS3BB5356
111PHEPHETRPTRP1AA54 - 5757 - 60
211PHEPHETRPTRP1BB54 - 5757 - 60
112VALVALVALVAL5AA5861
212VALVALVALVAL5BB5861
113PROPROPROPRO1AA6063
213PROPROPROPRO1BB6063
114ASNASNASNASN3AA6164
214ASNASNASNASN3BB6164
115LYSLYSGLUGLU4AA62 - 6765 - 70
215LYSLYSGLUGLU4BB62 - 6765 - 70
116LYSLYSASPASP1AA68 - 7771 - 80
216LYSLYSASPASP1BB68 - 7771 - 80
117PROPROASNASN4AA86 - 8789 - 90
217PROPROASNASN4BB86 - 8789 - 90
118ARGARGMETMET1AA88 - 13491 - 137
218ARGARGMETMET1BB88 - 13491 - 137
119HISHISHISHIS3AA135138
219HISHISHISHIS3BB135138
120GLUGLULEULEU1AA136 - 139139 - 142
220GLUGLULEULEU1BB136 - 139139 - 142
121ILEILEILEILE4AA140143
221ILEILEILEILE4BB140143
122ASPASPVALVAL2AA153 - 155156 - 158
222ASPASPVALVAL2BB153 - 155156 - 158
123CYSCYSLYSLYS1AA157 - 162160 - 165
223CYSCYSLYSLYS1BB157 - 162160 - 165
124GLNGLNGLNGLN3AA163166
224GLNGLNGLNGLN3BB163166

NCS oper: (Code: given
Matrix: (-0.99929, 0.035864, 0.011852), (0.034331, 0.99324, -0.11093), (-0.015751, -0.11044, -0.99376)
Vector: 60.738, 3.1051, 86.324)

-
Components

#1: Protein NO APICAL MERISTEM PROTEIN / NAM / ANAC / ABSCISIC ACID RESPONSIVE NAC


Mass: 19780.664 Da / Num. of mol.: 2 / Fragment: DNA-BINDING NAC DOMAIN, RESIDUES 1-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9C932
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNP_175697 (1-168) + EXTRA RESIDUE AT THE N-TERMINUS, ORIGINATING FROM A HIS-TAG SPACER REGION

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 30 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: Olsen, A., (2004) Acta Crystallogr.,Sect.D, 60, 112.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 %PEG40001reservoir
20.1 Mimidazole-malic acid1reservoirpH7.0
33.2-7.7 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.035
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 11476 / % possible obs: 95.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / % possible all: 89.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 89.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.857 / SU B: 9.623 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 652 5.1 %RANDOM
Rwork0.225 ---
obs0.228 12163 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 0 70 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222514
X-RAY DIFFRACTIONr_bond_other_d0.0020.022243
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.953395
X-RAY DIFFRACTIONr_angle_other_deg0.85935244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022712
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02541
X-RAY DIFFRACTIONr_nbd_refined0.1880.2406
X-RAY DIFFRACTIONr_nbd_other0.2370.22341
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.21483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7981.51473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52122376
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73731041
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9724.51019
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1433tight positional0.040.05
260medium positional0.370.5
107loose positional0.625
1433tight thermal0.10.5
260medium thermal0.492
107loose thermal1.7910
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.404 42
Rwork0.226 809
Refinement
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg6.8

+
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