[English] 日本語
Yorodumi
- PDB-3sy7: Improved crystal structure of Pseudomonas aeruginosa OprD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sy7
TitleImproved crystal structure of Pseudomonas aeruginosa OprD
ComponentsPorin D
KeywordsMEMBRANE PROTEIN / beta-barrel / channel / outer membrane
Function / homology
Function and homology information


basic amino acid transport / outer membrane / porin activity / pore complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / monoatomic ion transport / serine-type peptidase activity / cell outer membrane / proteolysis
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: 2.15 Å
Authorsvan den Berg, B. / Eren, E.
CitationJournal: Plos Biol. / Year: 2012
Title: Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
Authors: Eren, E. / Vijayaraghavan, J. / Liu, J. / Cheneke, B.R. / Touw, D.S. / Lepore, B.W. / Indic, M. / Movileanu, L. / van den Berg, B.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Porin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4029
Polymers46,9501
Non-polymers2,4528
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.408, 103.892, 47.544
Angle α, β, γ (deg.)90.00, 107.68, 90.00
Int Tables number5
Space group name H-MC121
DetailsProbable.

-
Components

#1: Protein Porin D / Imipenem/basic amino acid-specific outer membrane pore / Outer membrane protein D2


Mass: 46950.195 Da / Num. of mol.: 1 / Fragment: unp residues 24-443 / Mutation: V140F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: oprD, PA0958 / Production host: Escherichia coli (E. coli)
References: UniProt: P32722, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE STATED THAT THE RESIDUE 140 IS INDEED A VAL AND NOT A PHE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 2 M ammonium sulphate 50 mM Na-citrate, pH 5.5, VAPOR DIFFUSION, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 34239 / Num. obs: 33554 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.7
Reflection shellResolution: 2.15→2.19 Å / % possible all: 80.8

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.993 Å / SU ML: 0.68 / σ(F): 1.34 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 2001 5.97 %random
Rwork0.1956 ---
obs0.1974 33514 97.55 %-
all-34239 --
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.542 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3124 Å2-0 Å2-0.9502 Å2
2---10.145 Å2-0 Å2
3---5.8326 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 78 130 3177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073107
X-RAY DIFFRACTIONf_angle_d1.0724173
X-RAY DIFFRACTIONf_dihedral_angle_d19.8731111
X-RAY DIFFRACTIONf_chiral_restr0.079424
X-RAY DIFFRACTIONf_plane_restr0.004546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1488-2.20240.32441140.24691768X-RAY DIFFRACTION77
2.2024-2.26190.29871380.24692092X-RAY DIFFRACTION91
2.2619-2.32840.34471260.24932260X-RAY DIFFRACTION98
2.3284-2.40340.24021510.21142280X-RAY DIFFRACTION100
2.4034-2.48910.25421430.19662325X-RAY DIFFRACTION100
2.4891-2.58860.21711560.18352286X-RAY DIFFRACTION100
2.5886-2.70610.21291460.16832310X-RAY DIFFRACTION100
2.7061-2.84840.23551420.18292300X-RAY DIFFRACTION100
2.8484-3.02630.23991520.18172302X-RAY DIFFRACTION100
3.0263-3.25910.2051470.17462308X-RAY DIFFRACTION100
3.2591-3.58530.21361460.18312315X-RAY DIFFRACTION100
3.5853-4.10030.20721490.18712305X-RAY DIFFRACTION100
4.1003-5.15120.19861490.17642321X-RAY DIFFRACTION100
5.1512-19.99340.24051420.24172341X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2919-0.8262-0.29850.23530.24260.8148-0.09520.29970.1685-0.02450.0082-0.07880.04920.00860.15090.2003-0.0263-0.00940.24330.0330.248721.1303-8.4227-0.0965
22.0478-0.7588-0.01281.5299-0.06082.7473-0.15340.17140.18970.0530.0645-0.1817-0.04530.10250.13360.2022-0.0227-0.0020.27640.00520.231816.0535-10.456211.7003
31.77010.08020.25761.7323-0.02721.1167-0.0384-0.0122-0.02560.16870.05310.0350.0758-0.01940.00120.19310.03570.02640.1799-0.0070.116224.1743-14.905323.083
41.49310.4548-0.03120.78920.12131.8579-0.0795-0.0564-0.0251-0.02620.0025-0.07610.07720.22320.11380.18590.0443-0.01180.1894-0.02340.200338.2418-16.52415.7736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:121)
2X-RAY DIFFRACTION2chain 'A' and (resseq 122:158)
3X-RAY DIFFRACTION3chain 'A' and (resseq 159:304)
4X-RAY DIFFRACTION4chain 'A' and (resseq 305:421)

+
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