[English] 日本語
Yorodumi
- PDB-4kob: Investigating the functional significance of the interlocked pair... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kob
TitleInvestigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/V95I)
ComponentsAzurin
KeywordsELECTRON TRANSPORT / cupredoxin fold / computational protein design / copper binding
Function / homology
Function and homology information


transition metal ion binding / electron transfer activity / periplasmic space / 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: 1.867 Å
AuthorsInampudi, K.K. / Meng, W. / Tobin, P.H. / Wilson, C.J.
CitationJournal: To be Published
Title: Investigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/V95I)
Authors: Inampudi, K.K. / Meng, W. / Tobin, P.H. / Wilson, C.J.
History
DepositionMay 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Azurin
B: Azurin
C: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2148
Polymers55,9594
Non-polymers2544
Water14,664814
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0532
Polymers13,9901
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0532
Polymers13,9901
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0532
Polymers13,9901
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0532
Polymers13,9901
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.250, 97.220, 100.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Azurin /


Mass: 13989.853 Da / Num. of mol.: 4 / Fragment: UNP residues 21-148 / Mutation: V31I/V95I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl, 100 mM lithium nitrate, 10 mM copper sulfate, 30% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→30.85 Å / Num. obs: 42474 / % possible obs: 96.14 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.86 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.867→30.846 Å / SU ML: 0.21 / σ(F): 1.2 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 2144 5.07 %
Rwork0.1703 --
obs0.1731 42467 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1568 Å20 Å2-0 Å2
2--0.7195 Å20 Å2
3----0.8763 Å2
Refinement stepCycle: LAST / Resolution: 1.867→30.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 4 814 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073972
X-RAY DIFFRACTIONf_angle_d1.0465348
X-RAY DIFFRACTIONf_dihedral_angle_d12.8981452
X-RAY DIFFRACTIONf_chiral_restr0.074604
X-RAY DIFFRACTIONf_plane_restr0.004692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.867-1.88940.3127950.28811616X-RAY DIFFRACTION56
1.8894-1.91330.33821100.28141731X-RAY DIFFRACTION62
1.9133-1.93850.321160.25871946X-RAY DIFFRACTION69
1.9385-1.9650.32581400.24522174X-RAY DIFFRACTION76
1.965-1.99310.26171450.2322325X-RAY DIFFRACTION83
1.9931-2.02280.31061290.22372523X-RAY DIFFRACTION89
2.0228-2.05440.27831370.21072709X-RAY DIFFRACTION95
2.0544-2.08810.28241310.19872786X-RAY DIFFRACTION98
2.0881-2.12410.2611560.18032835X-RAY DIFFRACTION99
2.1241-2.16270.25831650.17572799X-RAY DIFFRACTION100
2.1627-2.20430.22271440.17472832X-RAY DIFFRACTION100
2.2043-2.24930.26921450.18192849X-RAY DIFFRACTION100
2.2493-2.29820.25591640.18222859X-RAY DIFFRACTION100
2.2982-2.35160.2231420.17182810X-RAY DIFFRACTION100
2.3516-2.41040.27171550.17522886X-RAY DIFFRACTION100
2.4104-2.47550.24561320.172822X-RAY DIFFRACTION100
2.4755-2.54840.2241860.17522832X-RAY DIFFRACTION100
2.5484-2.63060.21441740.16662804X-RAY DIFFRACTION100
2.6306-2.72450.25661340.15742850X-RAY DIFFRACTION100
2.7245-2.83360.20181420.16272861X-RAY DIFFRACTION100
2.8336-2.96240.20761240.16552880X-RAY DIFFRACTION100
2.9624-3.11850.24341250.16382860X-RAY DIFFRACTION100
3.1185-3.31360.22361460.15762862X-RAY DIFFRACTION100
3.3136-3.56910.19941170.14632862X-RAY DIFFRACTION100
3.5691-3.92770.16171660.14112818X-RAY DIFFRACTION100
3.9277-4.49450.15821520.13822825X-RAY DIFFRACTION100
4.4945-5.65690.20911400.1472843X-RAY DIFFRACTION100
5.6569-30.84990.19911690.18962767X-RAY DIFFRACTION98

+
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