[English] 日本語
Yorodumi
- PDB-6gyi: Azurin fom Pseudomonas aeruginosa treated with hydrosulfide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gyi
TitleAzurin fom Pseudomonas aeruginosa treated with hydrosulfide
ComponentsAzurin
KeywordsELECTRON TRANSPORT / copper protein / hydrosulfide sensor
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPalm, G.J. / Kohlhause, D.
CitationJournal: Eur J Inorg Chem / Year: 2019
Title: Azurin and HS-: towards implementation of a sensor for HS-detection.
Authors: Strianese, M. / Palm, G.J. / Kohlhause, D. / Ndamba, L.A. / Tabares, L.C. / Pellecchia , C.
History
DepositionJun 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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_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.ptnr1_symmetry / _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_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

-
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)56,26212
Polymers55,8474
Non-polymers4148
Water7,692427
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0653
Polymers13,9621
Non-polymers1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.736, 59.781, 79.727
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Azurin


Mass: 13961.799 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.18 Å3/Da / Density % sol: 44 % / Description: trapezoidal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 4000, 100 mM NaHEPES pH 6,5, 200 mM CaCl2, 10 mM Na2S. Cryoprotectant: 10% PEG 4000, 20% PEG 400, 100 mM NaHEPES pH 6,5, 200 mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.8141 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2017 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8141 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 62899 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.046 / Net I/σ(I): 10.8
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.015 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 9844 / CC1/2: 0.646 / Rrim(I) all: 1.099 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSNov 1, 2016data reduction
XDSNov 1, 2016data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZU

1azu


Resolution: 1.6→47.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0.005 / SU B: 5.794 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24273 2089 3.3 %RANDOM
Rwork0.19161 ---
obs0.1933 60454 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.679 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å2-0 Å2-0.36 Å2
2--1.23 Å20 Å2
3---1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.6→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 8 427 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0193977
X-RAY DIFFRACTIONr_bond_other_d0.0020.023604
X-RAY DIFFRACTIONr_angle_refined_deg2.7291.9495386
X-RAY DIFFRACTIONr_angle_other_deg1.30638449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1765523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70626.407167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54115706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.03154
X-RAY DIFFRACTIONr_chiral_restr0.180.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024454
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02722
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.0992050
X-RAY DIFFRACTIONr_mcbond_other1.1771.0982049
X-RAY DIFFRACTIONr_mcangle_it1.8321.642560
X-RAY DIFFRACTIONr_mcangle_other1.8321.6412561
X-RAY DIFFRACTIONr_scbond_it1.7471.2631927
X-RAY DIFFRACTIONr_scbond_other1.7471.2641928
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6171.8162818
X-RAY DIFFRACTIONr_long_range_B_refined5.99614.8194572
X-RAY DIFFRACTIONr_long_range_B_other5.92914.0254474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.34 152 3.5 %
Rwork0.305 4388 -
obs--98.42 %
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)
12.7095-0.427-0.38581.6477-0.09840.89090.13980.51890.2419-0.0063-0.127-0.1308-0.0306-0.1173-0.01280.27030.04420.02030.22670.07870.034811.00329.30811.947
22.1293-0.58751.31781.4243-1.3053.8870.20780.0169-0.0095-0.12620.11140.19280.31790.0878-0.31920.2105-0.0024-0.05150.03220.00880.046628.62728.45337.543
32.9128-1.9824-0.19683.5579-0.32781.9916-0.3266-0.5605-0.30480.3690.47970.2459-0.1543-0.0704-0.15310.26170.09250.05160.23450.08680.05013.23333.20852.305
41.3181-0.1998-0.9882.3467-1.59753.4979-0.0493-0.03560.0518-0.08950.123-0.16170.0489-0.1476-0.07370.214-0.02260.01590.0782-0.00620.028636.41532.44-1.885
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 128
2X-RAY DIFFRACTION2B2 - 128
3X-RAY DIFFRACTION3C1 - 128
4X-RAY DIFFRACTION4D2 - 128

+
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