[English] 日本語
Yorodumi
- PDB-1jzj: Pseudomonas aeruginosa Azurin Os(bpy)2(im)(His83) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jzj
TitlePseudomonas aeruginosa Azurin Os(bpy)2(im)(His83)
Componentsazurin
KeywordsELECTRON TRANSPORT / Blue-copper / electron transfer / tunneling / osmium
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 / DELTA-BIS(2,2'-BIPYRIDINE)IMIDAZOLE OSMIUM (II) / TETRA(IMIDAZOLE)DIAQUACOPPER (II) / LAMBDA-BIS(2,2'-BIPYRIDINE)IMIDAZOLE OSMIUM (II) / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCrane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: Electron tunneling in single crystals of Pseudomonas aeruginosa azurins.
Authors: Crane, B.R. / Di Bilio, A.J. / Winkler, J.R. / Gray, H.B.
History
DepositionSep 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_database_remark / Item: _diffrn_source.type / _pdbx_database_remark.text
Revision 1.4Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The osmium complex is BIS(2,2'-BIPYRIDINE)IMIDAZOLE OSMIUM (II) and is present in two ...HETEROGEN The osmium complex is BIS(2,2'-BIPYRIDINE)IMIDAZOLE OSMIUM (II) and is present in two enantiomeric conformations: delta, DOS, alternate conformation A, and lambda, LOS, alternate conformation B. For chain A, the DOS is residue number 903, and LOS is residue number 904. For chain B, the DOS is residue number 905, and LOS is residue number 906.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: azurin
B: azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,76110
Polymers27,9242
Non-polymers2,8378
Water4,828268
1
A: azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5335
Polymers13,9621
Non-polymers1,5714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2285
Polymers13,9621
Non-polymers1,2664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: azurin
B: azurin
hetero molecules

A: azurin
B: azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,52220
Polymers55,8474
Non-polymers5,67416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7170 Å2
ΔGint-55 kcal/mol
Surface area24120 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-20 kcal/mol
Surface area12250 Å2
MethodPISA
5
B: azurin
hetero molecules

B: azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,45610
Polymers27,9242
Non-polymers2,5338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1640 Å2
ΔGint-22 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.873, 54.873, 133.813
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-900-

CU

21A-1271-

HOH

DetailsBiological Assembly is a monomer

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein azurin /


Mass: 13961.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00282

-
Non-polymers , 5 types, 276 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-DOS / DELTA-BIS(2,2'-BIPYRIDINE)IMIDAZOLE OSMIUM (II)


Mass: 569.667 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19N6Os
#4: Chemical ChemComp-LOS / LAMBDA-BIS(2,2'-BIPYRIDINE)IMIDAZOLE OSMIUM (II)


Mass: 569.667 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19N6Os
#5: Chemical ChemComp-IME / TETRA(IMIDAZOLE)DIAQUACOPPER (II)


Mass: 367.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16CuN8O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG, Imidazole, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-30 mg/mlprotein1drop
240 mMimidazole1drop
32 mM1droppH7.2NaCl
4100 mMimidazole1reservoirpH6.0
5100 mM1reservoirLiNO3
66.25 mM1reservoirCuCl2
725-38 %PEG4000-80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 16, 2000 / Details: osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25.4 Å / Num. all: 21988 / Num. obs: 21988 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 21.1 Å2 / Rsym value: 0.072 / Net I/σ(I): 36
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14.8 % / Num. unique all: 2065 / Rsym value: 0.169 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.072

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JZI

1jzi


Resolution: 1.8→25.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 572477.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1729 7.9 %RANDOM
Rwork0.222 ---
all-21988 --
obs-21988 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.0465 Å2 / ksol: 0.323076 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0.68 Å20 Å2
2---1.52 Å20 Å2
3---3.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→25.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 146 268 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it0.31.5
X-RAY DIFFRACTIONc_mcangle_it0.542
X-RAY DIFFRACTIONc_scbond_it0.422
X-RAY DIFFRACTIONc_scangle_it0.552.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.287 166 8 %
Rwork0.259 1919 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMEWATER.TOP
X-RAY DIFFRACTION3OSA.PAROSA.TOP
X-RAY DIFFRACTION4WATER.PARAMTOPH19X.HEME
X-RAY DIFFRACTION5OSB.PAROSB.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7.9 % / Rfactor obs: 0.222 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
X-RAY DIFFRACTIONc_mcbond_it0.31.5
X-RAY DIFFRACTIONc_scbond_it0.422
X-RAY DIFFRACTIONc_mcangle_it0.542
X-RAY DIFFRACTIONc_scangle_it0.552.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.287 / % reflection Rfree: 8 % / Rfactor Rwork: 0.259

+
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