[English] 日本語
Yorodumi
- PDB-8wqz: X-ray Crystal Structure of Pseudoazurin Met16Gly variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wqz
TitleX-ray Crystal Structure of Pseudoazurin Met16Gly variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / Cu binding protein
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / DI(HYDROXYETHYL)ETHER / Pseudoazurin
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSugai, A. / Yamaguchi, T. / Kohzuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: X-ray Crystal Structure of Pseudoazurin Met16Gly variant
Authors: Sugai, A. / Yamaguchi, T. / Kohzuma, T.
History
DepositionOct 12, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 16, 2024ID: 5WV4
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2354
Polymers12,9591
Non-polymers2763
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, monomer state of WT was confirmed by ESI-MS and small angle neutron scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.181, 53.014, 59.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 12958.796 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: bcp / Production host: Escherichia coli (E. coli) / References: UniProt: P19567
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 42 %(w/v) PEG200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.2→39.47 Å / Num. obs: 31352 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.065 / Net I/σ(I): 21.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
6.57-39.474.20.05629.32360.9830.0410.0797.9
1.2-1.226.30.3058.114990.9590.1920.362

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata scaling
XDSdata reduction
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→39.47 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.006 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1526 1567 5.007 %
Rwork0.1311 29729 -
all0.132 --
obs-31296 99.758 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.593 Å2
Baniso -1Baniso -2Baniso -3
1-0.822 Å20 Å20 Å2
2---0.201 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.2→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 15 159 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121018
X-RAY DIFFRACTIONr_bond_other_d0.0010.016994
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.8351382
X-RAY DIFFRACTIONr_angle_other_deg0.6161.7692316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7215141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.20552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2210175
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1861038
X-RAY DIFFRACTIONr_chiral_restr0.0990.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021199
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02201
X-RAY DIFFRACTIONr_nbd_refined0.2680.2173
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.2892
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2470
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2108
X-RAY DIFFRACTIONr_metal_ion_refined0.1510.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3960.216
X-RAY DIFFRACTIONr_nbd_other0.2860.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.231
X-RAY DIFFRACTIONr_mcbond_it3.7920.952534
X-RAY DIFFRACTIONr_mcbond_other3.7840.952534
X-RAY DIFFRACTIONr_mcangle_it5.6521.719679
X-RAY DIFFRACTIONr_mcangle_other5.6521.719680
X-RAY DIFFRACTIONr_scbond_it5.0881.184484
X-RAY DIFFRACTIONr_scbond_other5.0841.186485
X-RAY DIFFRACTIONr_scangle_it7.2972.037701
X-RAY DIFFRACTIONr_scangle_other7.2922.039702
X-RAY DIFFRACTIONr_lrange_it12.99517.3191154
X-RAY DIFFRACTIONr_lrange_other11.91714.6251106
X-RAY DIFFRACTIONr_rigid_bond_restr3.86532012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2171130.1972152X-RAY DIFFRACTION99.9118
1.231-1.2650.2141130.1672095X-RAY DIFFRACTION99.9547
1.265-1.3010.1661100.1242056X-RAY DIFFRACTION99.8157
1.301-1.3410.171060.1131982X-RAY DIFFRACTION99.9521
1.341-1.3850.135970.1041944X-RAY DIFFRACTION99.8044
1.385-1.4340.1321130.0951872X-RAY DIFFRACTION100
1.434-1.4880.14990.0911828X-RAY DIFFRACTION99.9481
1.488-1.5490.142930.0961750X-RAY DIFFRACTION99.9458
1.549-1.6170.146790.0981669X-RAY DIFFRACTION99.8287
1.617-1.6960.145800.1031614X-RAY DIFFRACTION99.8232
1.696-1.7880.134840.1021531X-RAY DIFFRACTION99.7529
1.788-1.8960.126780.1041459X-RAY DIFFRACTION99.2253
1.896-2.0270.131750.1021371X-RAY DIFFRACTION99.9309
2.027-2.1890.139690.111289X-RAY DIFFRACTION100
2.189-2.3970.148590.1121197X-RAY DIFFRACTION99.7617
2.397-2.6780.135530.121082X-RAY DIFFRACTION99.8241
2.678-3.090.135480.137961X-RAY DIFFRACTION99.5069
3.09-3.7790.174520.147821X-RAY DIFFRACTION99.6575
3.779-5.320.172290.199665X-RAY DIFFRACTION99.1429
5.32-39.470.268170.343391X-RAY DIFFRACTION97.6077

+
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