[English] 日本語
Yorodumi
- PDB-6ap6: Crystal Structure of DAD2 in complex with tolfenamic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ap6
TitleCrystal Structure of DAD2 in complex with tolfenamic acid
ComponentsProbable strigolactone esterase DAD2
KeywordsPLANT PROTEIN / alpha/beta hydrolase
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-[(3-chloro-2-methylphenyl)amino]benzoic acid / Probable strigolactone esterase DAD2
Similarity search - Component
Biological speciesPetunia hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsHamiaux, C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
AGMARDT1323 New Zealand
MarsdenPAF1301 New Zealand
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Inhibition of strigolactone receptors byN-phenylanthranilic acid derivatives: Structural and functional insights.
Authors: Hamiaux, C. / Drummond, R.S.M. / Luo, Z. / Lee, H.W. / Sharma, P. / Janssen, B.J. / Perry, N.B. / Denny, W.A. / Snowden, K.C.
#1: Journal: Curr. Biol. / Year: 2012
Title: DAD2 is an alpha/beta hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone.
Authors: Hamiaux, C. / Drummond, R.S. / Janssen, B.J. / Ledger, S.E. / Cooney, J.M. / Newcomb, R.D. / Snowden, K.C.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Probable strigolactone esterase DAD2
B: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2964
Polymers59,7722
Non-polymers5232
Water8,737485
1
A: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1482
Polymers29,8861
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable strigolactone esterase DAD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1482
Polymers29,8861
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.860, 55.830, 69.230
Angle α, β, γ (deg.)95.760, 95.130, 108.460
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 3 - 266 / Label seq-ID: 5 - 268

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Probable strigolactone esterase DAD2 / Protein DECREASED APICAL DOMINANCE 2


Mass: 29886.164 Da / Num. of mol.: 2 / Mutation: C89Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petunia hybrida (garden petunia) / Gene: DAD2 / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami 2 / References: UniProt: J9U5U9
#2: Chemical ChemComp-TLF / 2-[(3-chloro-2-methylphenyl)amino]benzoic acid / Tolfenamic acid / Tolfenamic acid


Mass: 261.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12ClNO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.27 Å3/Da / Density % sol: 45.71 % / Description: Rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris/Acetate 0.1M, MgCl2 0.2M, PEG 8000 24%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→34.67 Å / Num. obs: 56704 / % possible obs: 91.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.683.80.86827610.6480.5151.0189.8
9.04-34.673.70.0283160.9980.0170.03383.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.18 Å30.42 Å
Translation5.18 Å30.42 Å

-
Processing

Software
NameVersionClassification
iMOSFLMdata processing
Aimless0.5.4data scaling
PHASER2.5.7phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNP

4dnp


Resolution: 1.65→30.42 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.764 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2868 5.1 %RANDOM
Rwork0.1681 ---
obs0.1697 53834 91.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 161.08 Å2 / Biso mean: 21.885 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0.33 Å20.15 Å2
2---0.97 Å2-0.18 Å2
3---0.92 Å2
Refinement stepCycle: final / Resolution: 1.65→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 36 485 4675
Biso mean--12 28.58 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194366
X-RAY DIFFRACTIONr_bond_other_d0.0060.024140
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9575951
X-RAY DIFFRACTIONr_angle_other_deg1.21239453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97622.549204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76315678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121538
X-RAY DIFFRACTIONr_chiral_restr0.0870.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215029
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021105
Refine LS restraints NCS

Ens-ID: 1 / Number: 32966 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 195 -
Rwork0.286 3969 -
all-4164 -
obs--89.99 %
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)
11.92680.19370.50210.69570.12271.4-0.0093-0.0850.0121-0.0126-0.0194-0.04930.0215-0.06350.02870.0047-0.02960.00870.2345-0.04690.025-16.4757.624-19.519
21.74240.24810.03960.99710.53361.36060.04730.1375-0.00420.04310.01490.0051-0.0409-0.0379-0.06220.0104-0.02390.00880.2563-0.05040.0191-13.52175.54615.522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 266
2X-RAY DIFFRACTION2B3 - 266

+
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