[English] 日本語
Yorodumi
- PDB-5bsv: Crystal structure of 4-coumarate:CoA ligase complexed with ferulo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bsv
TitleCrystal structure of 4-coumarate:CoA ligase complexed with feruloyl adenylate
Components4-coumarate--CoA ligase 2
KeywordsLIGASE / 4-coumarate:CoA ligase
Function / homology
Function and homology information


trans-feruloyl-CoA synthase / trans-feruloyl-CoA synthase activity / (E)-caffeate-CoA ligase activity / trans-cinnamate-CoA ligase activity / 4-coumarate-CoA ligase activity / 4-coumarate-CoA ligase / phenylpropanoid metabolic process / CoA-ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / response to jasmonic acid ...trans-feruloyl-CoA synthase / trans-feruloyl-CoA synthase activity / (E)-caffeate-CoA ligase activity / trans-cinnamate-CoA ligase activity / 4-coumarate-CoA ligase activity / 4-coumarate-CoA ligase / phenylpropanoid metabolic process / CoA-ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / response to jasmonic acid / response to wounding / ATP binding
Similarity search - Function
ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily ...ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4UW / 4-coumarate--CoA ligase 2
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLi, Z. / Nair, S.K.
CitationJournal: Structure / Year: 2015
Title: Structural Basis for Specificity and Flexibility in a Plant 4-Coumarate:CoA Ligase.
Authors: Li, Z. / Nair, S.K.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-coumarate--CoA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0692
Polymers59,5461
Non-polymers5231
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.441, 82.441, 181.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein 4-coumarate--CoA ligase 2 / 4CL 2 / 4-coumaroyl-CoA synthase 2


Mass: 59545.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: 4CL2 / Production host: Escherichia coli (E. coli) / References: UniProt: O24146, 4-coumarate-CoA ligase
#2: Chemical ChemComp-4UW / 5'-O-[(R)-hydroxy{[(2E)-3-(5-methoxy-4-oxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}phosphoryl]adenosine


Mass: 523.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N5O10P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25.5% w/v PEG 8000, 0.085 M sodium cacodylate pH 6.5, 0.17 M sodium acetate, and 15% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97947 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 69481 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.077 / Χ2: 1.92 / Net I/av σ(I): 41.545 / Net I/σ(I): 11.1 / Num. measured all: 498995
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.766.90.49968411.26799.8
1.76-1.837.20.38768601.282100
1.83-1.917.30.28168601.349100
1.91-2.027.30.20468901.497100
2.02-2.147.30.15268771.76100
2.14-2.317.30.12469202.06499.9
2.31-2.547.30.09869431.96499.9
2.54-2.917.30.07869732.09699.7
2.91-3.667.10.06670402.98799.3
3.66-506.90.05172772.89397.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0056refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.683 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 3503 5.1 %RANDOM
Rwork0.1894 ---
obs0.1903 65759 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 49.84 Å2 / Biso mean: 24.057 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4081 0 36 316 4433
Biso mean--17.62 32.13 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224204
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.9925709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3335528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96624.97169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30115727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2961517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213128
X-RAY DIFFRACTIONr_mcbond_it0.4431.52644
X-RAY DIFFRACTIONr_mcangle_it0.89124296
X-RAY DIFFRACTIONr_scbond_it1.61531560
X-RAY DIFFRACTIONr_scangle_it2.7294.51413
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 252 -
Rwork0.208 4780 -
all-5032 -
obs--99.74 %

+
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