[English] 日本語
Yorodumi
- PDB-4jdy: Crystal structure of Rv2606c -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jdy
TitleCrystal structure of Rv2606c
ComponentsPyridoxal biosynthesis lyase PdxS
KeywordsLYASE / (beta/alpha)8-barrel
Function / homology
Function and homology information


amine-lyase activity / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / amino acid metabolic process / plasma membrane
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxS / Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKim, S. / Kim, K.-J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase.
Authors: Kim, S. / Kim, K.J.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8356
Polymers83,5593
Non-polymers2763
Water8,017445
1
A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules

A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules

A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules

A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,34224
Polymers334,23712
Non-polymers1,10512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area39650 Å2
ΔGint-173 kcal/mol
Surface area103670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.752, 126.080, 180.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Pyridoxal biosynthesis lyase PdxS


Mass: 27853.072 Da / Num. of mol.: 3 / Fragment: UNP residues 11-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pdxS, Rv2606c, MT2681, MTCY1A10.27 / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P60796, UniProt: P9WII9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.78 Å3/Da / Density % sol: 67.43 % / Mosaicity: 0.28 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: PEG 8000, CAPS, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionRedundancy: 5.3 % / Av σ(I) over netI: 20.19 / Number: 609007 / Rmerge(I) obs: 0.072 / Χ2: 0.98 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 115287 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.610.0441.5476.3
3.083.8899.710.0521.2836.4
2.693.0899.410.0731.0595.8
2.442.6999.410.0950.9795.7
2.272.4499.410.1190.9075.4
2.132.2799.210.1470.8345.3
2.032.1399.310.1890.7915.1
1.942.0398.910.2380.6834.7
1.861.9498.410.2910.5854.2
1.81.869710.3280.5493.8
ReflectionResolution: 1.8→50 Å / Num. obs: 115287 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.072 / Χ2: 0.978 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.80.328112280.549197
1.86-1.944.20.291113170.585198.4
1.94-2.034.70.238114330.683198.9
2.03-2.135.10.189114650.791199.3
2.13-2.275.30.147114910.834199.2
2.27-2.445.40.119115020.907199.4
2.44-2.695.70.095115720.979199.4
2.69-3.085.80.073116001.059199.4
3.08-3.886.40.052116821.283199.7
3.88-506.30.044119971.547199.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ISS

2iss


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1898 / WRfactor Rwork: 0.1651 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8912 / SU B: 1.967 / SU ML: 0.061 / SU R Cruickshank DPI: 0.092 / SU Rfree: 0.0929 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / 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
Rfree0.2106 5765 5 %RANDOM
Rwork0.1829 ---
obs0.1843 115269 99 %-
all-153419 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.74 Å2 / Biso mean: 23.2308 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5841 0 18 445 6304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0225943
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.9688037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27723.421228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9871548
X-RAY DIFFRACTIONr_chiral_restr0.1810.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214425
X-RAY DIFFRACTIONr_mcbond_it1.6051.53915
X-RAY DIFFRACTIONr_mcangle_it2.7126255
X-RAY DIFFRACTIONr_scbond_it4.02432028
X-RAY DIFFRACTIONr_scangle_it6.2494.51782
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 396 -
Rwork0.278 7803 -
all-8199 -
obs--95.98 %

+
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