[English] 日本語
Yorodumi
- PDB-4fsp: Crystal Structure of Pseudomonas aeruginosa OccK11 (OpdR) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fsp
TitleCrystal Structure of Pseudomonas aeruginosa OccK11 (OpdR)
ComponentsProbable porin
KeywordsTRANSPORT PROTEIN / Beta-barrel / Transporter (porin) / Outer Membrane
Function / homology
Function and homology information


porin activity / membrane
Similarity search - Function
Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.323 Å
AuthorsEren, E. / van den Berg, B.
CitationJournal: To be Published
Title: Crystal Structures of OccK Subfamily Proteins
Authors: Eren, E. / van den Berg, B.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,99810
Polymers45,2401
Non-polymers2,7589
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.892, 147.810, 84.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

-
Components

#1: Protein Probable porin


Mass: 45240.152 Da / Num. of mol.: 1 / Fragment: unp residues 23-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3588 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HY38
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG 4000, 0.2M potassium fluoride, 0.05M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.897 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.897 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 26201 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rsym value: 0.072 / Net I/σ(I): 33.1
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1288 / Rsym value: 0.628 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T20

3t20


Resolution: 2.323→19.948 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1327 5.08 %
Rwork0.1936 --
obs0.196 26141 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.323→19.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 105 159 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073030
X-RAY DIFFRACTIONf_angle_d1.2324042
X-RAY DIFFRACTIONf_dihedral_angle_d17.8991144
X-RAY DIFFRACTIONf_chiral_restr0.084403
X-RAY DIFFRACTIONf_plane_restr0.005524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3233-2.41610.27671500.21652645X-RAY DIFFRACTION98
2.4161-2.52590.31891380.21452745X-RAY DIFFRACTION100
2.5259-2.65880.23911460.19782744X-RAY DIFFRACTION100
2.6588-2.82490.26311610.19512713X-RAY DIFFRACTION100
2.8249-3.04240.25921310.18942777X-RAY DIFFRACTION100
3.0424-3.34720.22911530.1922723X-RAY DIFFRACTION100
3.3472-3.82860.23811290.18482811X-RAY DIFFRACTION100
3.8286-4.81240.21731560.18062765X-RAY DIFFRACTION100
4.8124-19.94850.24041630.20742891X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -29.1167 Å / Origin y: 24.4604 Å / Origin z: -2.3814 Å
111213212223313233
T0.2131 Å2-0.0276 Å2-0.0659 Å2-0.217 Å20.0191 Å2--0.2079 Å2
L0.5124 °20.3669 °2-0.6038 °2-1.4779 °2-0.9471 °2--1.6621 °2
S-0.08 Å °0.0638 Å °-0.0829 Å °-0.2441 Å °0.1448 Å °0.1014 Å °0.3151 Å °-0.1532 Å °-0.0524 Å °
Refinement TLS groupSelection details: all

+
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