[English] 日本語
Yorodumi
- PDB-4ldw: Crystal structure of the DNA Binding Domain of arabidopsis thalia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ldw
TitleCrystal structure of the DNA Binding Domain of arabidopsis thaliana auxin response factor 1, P21 structure
ComponentsAuxin response factor 1
KeywordsTRANSCRIPTION / Transcription factor / Dna binding / nucleus
Function / homology
Function and homology information


leaf senescence / cell death / response to auxin / auxin-activated signaling pathway / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
SH3 type barrels. - #1040 / Auxin response factor domain / Auxin response factor / Auxin response factor ancillary domain / DNA-binding pseudobarrel domain / At1g16640 B3 domain / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain ...SH3 type barrels. - #1040 / Auxin response factor domain / Auxin response factor / Auxin response factor ancillary domain / DNA-binding pseudobarrel domain / At1g16640 B3 domain / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / : / PB1 domain profile. / SH3 type barrels. / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Auxin response factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
Authorsboer, D.R. / Coll, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors.
Authors: Boer, D.R. / Freire-Rios, A. / van den Berg, W.A. / Saaki, T. / Manfield, I.W. / Kepinski, S. / Lopez-Vidrieo, I. / Franco-Zorrilla, J.M. / de Vries, S.C. / Solano, R. / Weijers, D. / Coll, M.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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 / _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: Auxin response factor 1
B: Auxin response factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2304
Polymers82,1592
Non-polymers712
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-35 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.260, 83.670, 79.027
Angle α, β, γ (deg.)90.00, 117.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Auxin response factor 1


Mass: 41079.363 Da / Num. of mol.: 2 / Fragment: DNA Binding Domain, UNP residues 1-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARF1, At1g59750, auxin response factor 1, F23H11.7 / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q8L7G0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 4 mg/mL ARF1DBD + 1 l crystallization buffer (100 mM MES 6.5, 20%PEG 5K MME) 7.7.11), VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.67→70.02 Å / Num. obs: 23332 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 73.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.9
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3391 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LDV

4ldv


Resolution: 2.67→35.94 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 31.115 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 1.1 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27945 1173 5 %RANDOM
Rwork0.21561 ---
obs0.21885 22140 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.443 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å21.32 Å2
2---2.85 Å2-0 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.67→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 2 54 5160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195236
X-RAY DIFFRACTIONr_bond_other_d0.0010.024900
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9417092
X-RAY DIFFRACTIONr_angle_other_deg0.772311278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69322.691249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58915882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7091548
X-RAY DIFFRACTIONr_chiral_restr0.0810.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021263
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_it1.7563.0392530
X-RAY DIFFRACTIONr_mcbond_other1.7553.0392529
X-RAY DIFFRACTIONr_mcangle_it2.9394.5533145
X-RAY DIFFRACTIONr_mcangle_other2.9394.5533146
X-RAY DIFFRACTIONr_scbond_it1.873.2272706
X-RAY DIFFRACTIONr_scbond_other1.8693.2282707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0894.763948
X-RAY DIFFRACTIONr_long_range_B_refined5.46624.1235775
X-RAY DIFFRACTIONr_long_range_B_other5.46424.1025772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.667→2.736 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 86 -
Rwork0.32 1598 -
obs--94.61 %
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)
16.3767-0.1179-3.54973.39380.68346.06820.0487-0.22590.03530.0675-0.1479-0.1462-0.09520.07130.09920.20910.0056-0.01260.12950.07090.07111.102721.519234.9411
23.9377-0.7756-5.09591.68520.37726.8933-0.1161-0.1203-0.08880.34720.03440.2469-0.09270.07810.08170.50320.04240.03550.446-0.02960.3603-8.57522.243558.6748
33.72770.2561-5.67110.7315-0.90359.0299-0.21630.1946-0.11380.12790.13520.20270.1923-0.46040.08110.24690.05930.01490.3178-0.04570.2304-2.832919.974242.9907
45.1113-10.47980.859821.6243-1.85640.3291-0.4651-0.2734-0.03830.97160.3453-0.18360.12360.20740.11980.50160.0924-0.0520.55830.28410.586721.796711.019739.5242
59.583-0.1619-1.78889.6323-2.16825.90520.02930.0161-0.1224-0.24050.0625-0.11790.2466-0.0263-0.09180.36380.04450.01960.20750.07780.368613.41991.251339.7307
610.61550.0287-2.10011.5722-1.50431.8547-0.0907-0.0146-0.1099-0.18210.019-0.04830.1614-0.06830.07170.23330.05550.02030.1924-0.02990.2629-7.645324.00667.1824
710.4321-0.0427-2.08041.1207-0.4861.29610.123-0.0306-0.34330.091-0.05430.10980.0462-0.0141-0.06870.32480.0228-0.0780.2263-0.03080.3867-9.573821.8925.5857
810.3543-0.8917-0.51341.7142-0.41621.51020.11420.0093-0.6540.0757-0.1014-0.24050.05210.0997-0.01280.2252-0.0615-0.01080.2971-0.00330.2541-35.318320.61213.6596
93.5585-1.32271.00661.80051.27262.55320.07590.1338-0.0362-0.2849-0.12820.2022-0.1968-0.14880.05230.2058-0.0106-0.02810.25470.00930.2887-0.559325.82385.9895
109.9182-2.47-0.19079.5875-2.21666.7891-0.11970.16460.39590.11510.0481-0.2574-0.17740.16860.07170.38940.0413-0.03890.16350.00080.4033-8.185841.8652.4886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 107
2X-RAY DIFFRACTION2A108 - 181
3X-RAY DIFFRACTION3A182 - 271
4X-RAY DIFFRACTION4A272 - 290
5X-RAY DIFFRACTION5A291 - 356
6X-RAY DIFFRACTION6B16 - 63
7X-RAY DIFFRACTION7B64 - 139
8X-RAY DIFFRACTION8B140 - 234
9X-RAY DIFFRACTION9B235 - 288
10X-RAY DIFFRACTION10B289 - 355

+
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