[English] 日本語
Yorodumi
- PDB-2q4d: Ensemble refinement of the crystal structure of a lysine decarbox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q4d
TitleEnsemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950
ComponentsLysine decarboxylase-like protein At5g11950
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / AT5G11950 / LYSINE DECARBOXYLASE-LIKE PROTEIN / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process / protein homodimerization activity / nucleus / plasma membrane / cytosol
Similarity search - Function
Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG / LOG family / Possible lysine decarboxylase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.152 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
#1: Journal: Proteins / Year: 2006
Title: X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and AT2g37210.
Authors: Jeon, W.B. / Allard, S.T.M. / Bingman, C.A. / Bitto, E. / Han, B.W. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine decarboxylase-like protein At5g11950
B: Lysine decarboxylase-like protein At5g11950
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7897
Polymers48,4782
Non-polymers3105
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-22 kcal/mol
Surface area14760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.589, 80.427, 50.709
Angle α, β, γ (deg.)90.000, 102.970, 90.000
Int Tables number5
Space group name H-MC121
Number of models16
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

22A-850-

HOH

33A-852-

HOH

44A-850-

HOH

55A-857-

HOH

66A-848-

HOH

77A-854-

HOH

88A-853-

HOH

99A-857-

HOH

1010A-846-

HOH

1111A-846-

HOH

1212A-847-

HOH

1313A-850-

HOH

1414A-849-

HOH

1515A-850-

HOH

1616A-853-

HOH

-
Components

#1: Protein Lysine decarboxylase-like protein At5g11950


Mass: 24239.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: AT5G11950, F14F18.120 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) P(LACI+RARE) / References: UniProt: Q84MC2
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.63 %
Description: AUTHOR USED THE SF DATA FROM ENTRY 1YDH. UNMODELED DENSITY BETWEEN ASP 94A AND ILE 133B IS POSSIBLY DUE TO THE PRESENCE OF A L-LYSINE MOLECULE.

-
Data collection

DetectorType: APS-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 1YDH

1ydh


Resolution: 2.152→34.35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2526756.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1ydh and the first data set in the deposited structure factor file for 1ydh ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1ydh and the first data set in the deposited structure factor file for 1ydh along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1300 5.1 %RANDOM
Rwork0.152 ---
obs0.152 25678 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.046 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å21.17 Å2
2--0 Å20 Å2
3----1.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.152→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 20 319 3135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.152-2.290.2332014.90.16439400.0164313414196
2.29-2.460.2392185.10.15940630.0164294428199.7
2.46-2.710.2312185.10.14940650.0164305428399.5
2.71-3.10.2112225.20.15240630.0144310428599.4
3.1-3.910.2042205.10.15240900.0144334431099.4
3.91-34.340.18722150.14841570.0134385437899.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3edo.param
X-RAY DIFFRACTION4no3.par

+
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