[English] 日本語
Yorodumi
- PDB-5y23: X-ray crystal structure of Pseudoazurin Met16Phe variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y23
TitleX-ray crystal structure of Pseudoazurin Met16Phe variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / Electron transfer / Cupredoxin
Function / homology
Function and homology information


electron transfer activity / periplasmic space / 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. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...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. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Pseudoazurin
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsYamaguchi, T. / Akao, K. / Kohzuma, T.
CitationJournal: To Be Published
Title: X-ray crystal structure of Pseudoazurin Met16Phe variant
Authors: Yamaguchi, T. / Akao, K. / Kohzuma, T.
History
DepositionJul 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pseudoazurin
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,77710
Polymers26,0982
Non-polymers6808
Water5,729318
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3895
Polymers13,0491
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-0 kcal/mol
Surface area6320 Å2
MethodPISA
2
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3895
Polymers13,0491
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-1 kcal/mol
Surface area6040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.715, 59.620, 54.324
Angle α, β, γ (deg.)90.000, 105.370, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 13048.918 Da / Num. of mol.: 2 / Mutation: M16F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: bcp / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19567
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Drop: 100 mM Tris-HCl buffer, 15.5 % PEG4000, 31 mg/mL Protein Reservoir: 100 mM Tris-HCl buffer, 31 % PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 40971 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Χ2: 0.999 / Net I/σ(I): 9.8 / Num. measured all: 154641
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.4-1.453.70.2310.507196
1.45-1.513.80.1740.552196.5
1.51-1.583.80.140.598197
1.58-1.663.80.110.635197.3
1.66-1.763.80.0930.71197.7
1.76-1.93.80.0740.877198.1
1.9-2.093.80.0611.12198.5
2.09-2.393.80.0551.303199
2.39-3.023.80.0481.502199.3
3.02-503.60.0472.223194.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 1.4→26.2 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.707 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.064
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 2069 5.1 %RANDOM
Rwork0.141 ---
obs0.143 38882 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.3 Å2 / Biso mean: 15.307 Å2 / Biso min: 4.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.15 Å2
2--0.25 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 1.4→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 50 353 2235
Biso mean--27.92 28.14 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192039
X-RAY DIFFRACTIONr_bond_other_d0.0020.022028
X-RAY DIFFRACTIONr_angle_refined_deg2.6431.9892762
X-RAY DIFFRACTIONr_angle_other_deg1.13934721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7955278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89426.16473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47915353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.793152
X-RAY DIFFRACTIONr_chiral_restr0.1520.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212330
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
LS refinement shellResolution: 1.4→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 164 -
Rwork0.184 2802 -
all-2966 -
obs--94.85 %
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)
11.19540.36040.13381.15390.17340.7485-0.02260.0482-0.0248-0.02930.0255-0.0331-0.01790.03-0.00290.0614-0.00670.00970.0038-0.0010.00411.90680.309721.846
21.88630.08050.09930.43420.06970.76190.0574-0.07190.02080.0245-0.0518-0.0319-0.0086-0.0071-0.00550.0435-0.00640.010.0170.00760.008828.02682.1242-2.4259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2B1 - 124

+
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