[English] 日本語
Yorodumi
- PDB-5z0x: X-ray Crystal Structure of Pseudoazurin Met16Tyr Variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z0x
TitleX-ray Crystal Structure of Pseudoazurin Met16Tyr Variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT
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. / 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 / molecular replacement / Resolution: 1.46 Å
AuthorsSaito, Y. / Yamaguchi, T. / Kohzuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science22550145 Japan
CitationJournal: To Be Published
Title: X-ray Crystal Structure of Pseudoazurin Met16Tyr Variant
Authors: Yamaguchi, T. / Saito, Y. / Kohzuma, T.
History
DepositionDec 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 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)26,4416
Polymers26,1302
Non-polymers3114
Water5,945330
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2213
Polymers13,0651
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area6030 Å2
MethodPISA
2
B: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2213
Polymers13,0651
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.540, 59.030, 54.000
Angle α, β, γ (deg.)90.000, 105.560, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 13064.918 Da / Num. of mol.: 2 / Mutation: M16Y
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.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, 34% PEG4000, 45mg/mL Protein

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→52.021 Å / Num. all: 29007 / Num. obs: 29007 / % possible obs: 80.8 % / Redundancy: 3.3 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Rsym value: 0.068 / Net I/av σ(I): 8.1 / Net I/σ(I): 9.3 / Num. measured all: 95447
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.46-1.543.30.357240590.2270.4250.35777.6
1.54-1.633.40.2483.137980.1560.2940.24876.8
1.63-1.753.40.23.735480.1250.2370.276.5
1.75-1.883.30.145.132850.0880.1650.1476.3
1.88-2.063.30.1116.130270.070.1320.11176.3
2.06-2.313.20.097.429330.0570.1070.0981.5
2.31-2.673.10.0748.728570.0470.0880.07488.8
2.67-3.263.40.05512.424970.0340.0640.05592.4
3.26-4.623.40.0416.619540.0250.0480.0492.8
4.62-28.2873.10.03319.310490.0210.0390.03388.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.53
Highest resolutionLowest resolution
Rotation28.29 Å1.65 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YL4

4yl4


Resolution: 1.46→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.443 / SU ML: 0.054 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.086
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 1469 5.1 %RANDOM
Rwork0.1457 ---
obs0.1481 27501 79.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.97 Å2 / Biso mean: 16.111 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.46→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 14 330 2178
Biso mean--19.66 28.59 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191905
X-RAY DIFFRACTIONr_bond_other_d0.0030.021854
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9712577
X-RAY DIFFRACTIONr_angle_other_deg1.07434297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69926.11172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.173152
X-RAY DIFFRACTIONr_chiral_restr0.130.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212173
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02385
LS refinement shellResolution: 1.46→1.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 85 -
Rwork0.233 1962 -
all-2047 -
obs--76.49 %

+
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