[English] 日本語
Yorodumi
- PDB-2oj1: Disulfide-linked dimer of azurin N42C/M64E double mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oj1
TitleDisulfide-linked dimer of azurin N42C/M64E double mutant
ComponentsAzurin
KeywordsELECTRON TRANSPORT / cupredoxin / electron transfer / engineered dimer
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding
Similarity search - Function
Azurin / : / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsde Jongh, T.E. / Hoffmann, M. / Einsle, O. / Cavazzini, D. / Rossi, G.L. / Ubbink, M. / Canters, G.W.
CitationJournal: Eur.J.Inorg.Chem. / Year: 2007
Title: Inter- and intramolecular electron transfer in modified azurin dimers
Authors: de Jongh, T.E. / Hoffmann, M. / Einsle, O. / Cavazzini, D. / Rossi, G.L. / Ubbink, M. / Canters, G.W.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0254
Polymers27,8982
Non-polymers1272
Water2,738152
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0122
Polymers13,9491
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0122
Polymers13,9491
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.570, 116.980, 30.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Azurin


Mass: 13948.757 Da / Num. of mol.: 2 / Mutation: N42C, M64E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Plasmid: pTJ01 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.1
Details: 30 % PEG 4000, 0.1M sodium citrate buffer, pH 3.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2004 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→34.3 Å / Num. all: 10903 / Num. obs: 10369 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.88 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1405 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOLREPphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P. aeruginosa azurin wildtype

Resolution: 2.3→34.3 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 725 -random
Rwork0.208 ---
all-10903 --
obs-10369 95.1 %-
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.959 Å20 Å20 Å2
2--10.566 Å20 Å2
3----11.526 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 2 152 2100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_angle_deg2.843

+
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