[English] 日本語
Yorodumi
- PDB-5gjm: Crystal structure of Lysine decarboxylase from Selenomonas rumina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gjm
TitleCrystal structure of Lysine decarboxylase from Selenomonas ruminantium in C2 space group
ComponentsLysine/ornithine decarboxylase
KeywordsLYASE / barrel domain
Function / homology
Function and homology information


ornithine decarboxylase / lysine decarboxylase / lysine decarboxylase activity / putrescine biosynthetic process from arginine, via ornithine / ornithine decarboxylase activity / spermidine biosynthetic process / cytoplasm
Similarity search - Function
Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Ornithine decarboxylase / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lysine/ornithine decarboxylase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.91 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: PLoS ONE / Year: 2016
Title: Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium
Authors: Sagong, H.-Y. / Son, H.F. / Kim, S. / Kim, Y.-H. / Kim, I.-K. / Kim, K.-J.
History
DepositionJul 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine/ornithine decarboxylase
B: Lysine/ornithine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6193
Polymers86,5272
Non-polymers921
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-24 kcal/mol
Surface area29270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.450, 70.794, 88.061
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Lysine/ornithine decarboxylase / LDC / PLP binding barrel domain


Mass: 43263.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Strain: ATCC12561 / Gene: ldc / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21T1R / References: UniProt: O50657, lysine decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.59 Å3/Da / Density % sol: 52.49 % / Mosaicity: 1.464 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Sodium citrate, Sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2014
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 18678 / % possible obs: 95.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.145 / Net I/av σ(I): 23.9 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.9-2.953.30.3460.67194.2
2.95-33.40.3140.731194.9
3-3.063.30.2730.759194.5
3.06-3.123.30.2290.875195.4
3.12-3.193.30.2070.936195.6
3.19-3.273.30.1880.936193.8
3.27-3.353.20.1650.939195.4
3.35-3.443.20.1580.955193.2
3.44-3.543.20.1470.964194.3
3.54-3.653.80.1880.951196.3
3.65-3.783.80.1850.926197.3
3.78-3.943.40.1310.972193.6
3.94-4.113.50.1150.978194.9
4.11-4.333.80.1160.977196.5
4.33-4.63.80.1030.979195.6
4.6-4.963.70.0980.985194.8
4.96-5.463.80.1020.978196.1
5.46-6.243.80.1140.975196.8
6.24-7.863.90.0960.983197
7.86-504.20.080.989193

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PLJ

2plj


Resolution: 2.91→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.861 / SU B: 15.146 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23364 930 5 %RANDOM
Rwork0.17716 ---
obs0.18125 17748 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.219 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å20.3 Å2
2--3.2 Å2-0 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5785 0 6 122 5913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195915
X-RAY DIFFRACTIONr_bond_other_d0.0020.025639
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9698003
X-RAY DIFFRACTIONr_angle_other_deg1.024312992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2995745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09423.852257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49715984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2661535
X-RAY DIFFRACTIONr_chiral_restr0.0880.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216677
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021322
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_it1.3742.0412992
X-RAY DIFFRACTIONr_mcbond_other1.3742.0412991
X-RAY DIFFRACTIONr_mcangle_it2.453.0543733
X-RAY DIFFRACTIONr_mcangle_other2.453.0553734
X-RAY DIFFRACTIONr_scbond_it1.382.1972923
X-RAY DIFFRACTIONr_scbond_other1.382.1972923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4033.2084271
X-RAY DIFFRACTIONr_long_range_B_refined4.50123.326353
X-RAY DIFFRACTIONr_long_range_B_other4.50123.3256354
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.906→2.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 61 -
Rwork0.195 1218 -
obs--88.76 %

+
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