[English] 日本語
Yorodumi
- PDB-2pst: 1.8A Crystal Structure of the PA2412 protein from Pseudomonas aer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pst
Title1.8A Crystal Structure of the PA2412 protein from Pseudomonas aeruginosa
ComponentsHypothetical protein PA2412
KeywordsUNKNOWN FUNCTION / Pyoverdine synthesis / Non-ribosomal peptide synthesis clusters / MbtH-like family / COG3251
Function / homology
Function and homology information


pyoverdine biosynthetic process / siderophore biosynthetic process / cytosol
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MbtH-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsGulick, A.M. / Drake, E.J. / Shah, M.B.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The 1.8 A crystal structure of PA2412, an MbtH-like protein from the pyoverdine cluster of Pseudomonas aeruginosa.
Authors: Drake, E.J. / Cao, J. / Qu, J. / Shah, M.B. / Straubinger, R.M. / Gulick, A.M.
History
DepositionMay 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Hypothetical protein PA2412


Theoretical massNumber of molelcules
Total (without water)8,6501
Polymers8,6501
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.543, 51.543, 32.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Hypothetical protein PA2412


Mass: 8649.739 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Plasmid: pET15 modified / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I169
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5
Details: Microbatch 1:1 with 33-37% polyethylene propoxylate 426, 50 mM Succinate, pH 5.0, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11131
21
31
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONCHESS F210.97931
SYNCHROTRONCHESS F220.97910, 0.97934, 0.9641
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 30, 2005
ADSC QUANTUM 2102CCDNov 20, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CHESS F2SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.97911
30.979341
40.96411
Reflection

D res high: 1.9 Å / D res low: 25 Å / % possible obs: 99.9

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs
4.6115.1315940.0784.186914
4.5221.6313620.0431.696917
4.7319.9322930.0562.856916
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.092599.210.06710.184.5
3.254.0999.710.0656.6854.7
2.843.2510010.0785.5124.8
2.582.8410010.0934.724.8
2.392.5810010.13.7764.7
2.252.3910010.0982.7974.6
2.142.2510010.1062.5694.5
2.052.1410010.1071.6734.4
1.972.0599.910.121.6194.4
1.91.9799.910.1411.244.3
4.092599.620.0342.5154.5
3.254.0999.720.0352.0794.7
2.843.2510020.041.8964.7
2.582.8410020.0481.8144.7
2.392.5810020.0571.6964.7
2.252.3910020.0611.554.5
2.142.2510020.0691.5164.5
2.052.1410020.0781.3684.4
1.972.0599.920.0881.1874.3
1.91.9799.920.1131.1444.3
4.092599.530.0457.1784.6
3.254.0999.730.0453.754.8
2.843.2510030.0563.2624.9
2.582.8410030.0652.9524.9
2.392.5810030.0732.5274.8
2.252.3910030.0772.0974.7
2.142.2599.930.0851.8744.6
2.052.1410030.0991.6264.5
1.972.0510030.1051.3674.5
1.91.9799.930.1411.3064.4
ReflectionResolution: 1.8→27.5 Å / Num. obs: 7822 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.072 / Χ2: 0.977 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.3 / Num. unique all: 574 / Χ2: 0.521 / % possible all: 72.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CHESSF2data collection
HKL-2000data reduction
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→27.5 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.154 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 359 4.6 %RANDOM
Rwork0.192 ---
obs0.194 7809 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.293 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms509 0 0 76 585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022527
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.934715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.677562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93724.64328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5461593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.199153
X-RAY DIFFRACTIONr_chiral_restr0.0960.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02408
X-RAY DIFFRACTIONr_nbd_refined0.1930.2195
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.210
X-RAY DIFFRACTIONr_mcbond_it0.7841.5320
X-RAY DIFFRACTIONr_mcangle_it1.2222496
X-RAY DIFFRACTIONr_scbond_it1.7273251
X-RAY DIFFRACTIONr_scangle_it2.7034.5218
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 14 -
Rwork0.253 415 -
obs-429 70.56 %
Refinement TLS params.Method: refined / Origin x: 2.264 Å / Origin y: 36.139 Å / Origin z: 20.374 Å
111213212223313233
T-0.0388 Å20.0016 Å2-0.0159 Å2--0.0727 Å2-0.0117 Å2---0.0818 Å2
L0.5519 °20.7267 °20.316 °2-3.514 °22.7308 °2--3.0742 °2
S-0.0561 Å °-0.0323 Å °-0.0331 Å °-0.0131 Å °0.1224 Å °-0.0751 Å °-0.068 Å °0.0871 Å °-0.0663 Å °

+
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://pdbjlvh1.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