[English] 日本語
Yorodumi
- PDB-6ifp: X-ray Crystal Structure of Pseudoazurin Met16Ile Variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ifp
TitleX-ray Crystal Structure of Pseudoazurin Met16Ile Variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II 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 / molecular replacement / Resolution: 1 Å
AuthorsSakai, C. / 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 Met16Leu Variant
Authors: Sakai, C. / Yamaguchi, T. / Kohzuma, T.
History
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: 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
C: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1574
Polymers26,0302
Non-polymers1272
Water9,836546
1
A: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0782
Polymers13,0151
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0782
Polymers13,0151
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.956, 60.183, 47.988
Angle α, β, γ (deg.)90.000, 96.160, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 13014.902 Da / Num. of mol.: 2 / Fragment: UNP residues 29-152 / Mutation: M16I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: bcp / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 1.87 Å3/Da / Density % sol: 34.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris-HCl, 35 % PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 103433 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Χ2: 1.826 / Net I/σ(I): 8 / Num. measured all: 737381
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1-1.0260.80151160.7830.3450.8750.91399.8
1.02-1.046.60.73751380.8420.3080.8011.003100
1.04-1.066.80.60751820.8670.2510.6581.165100
1.06-1.086.90.49351290.9160.2030.5341.247100
1.08-1.170.40851680.9430.1670.4411.258100
1.1-1.1370.34551630.9570.1410.3741.415100
1.13-1.157.10.29651440.970.1210.3211.435100
1.15-1.197.10.27751670.9710.1120.31.576100
1.19-1.227.10.2451520.9790.0970.2591.543100
1.22-1.267.20.24152200.9760.0970.2611.819100
1.26-1.37.20.22651610.9770.0910.2441.952100
1.3-1.367.30.18251400.9860.0730.1961.626100
1.36-1.427.30.17551720.9850.070.1892.016100
1.42-1.497.40.1451580.9920.0560.1511.953100
1.49-1.597.40.12151690.9940.0480.132.239100
1.59-1.717.40.0952170.9950.0360.0971.909100
1.71-1.887.50.07751670.9970.030.0822.051100
1.88-2.157.50.07352070.9970.0280.0783.078100
2.15-2.717.50.06151940.9970.0240.0652.756100
2.71-507.20.05152690.9960.0210.0553.00599.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.661
Highest resolutionLowest resolution
Rotation20.55 Å1.21 Å

-
Processing

Software
NameVersionClassificationNB
SHELXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 1→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1436 5281 -
Rwork0.1103 --
obs-103282 99.9 %
Displacement parametersBiso max: 112.58 Å2 / Biso mean: 15.1194 Å2 / Biso min: 3.37 Å2
Refinement stepCycle: LAST / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 2 546 2374
LS refinement shellResolution: 1→1.04 Å /
RfactorNum. reflection
Rwork0.229 -
obs-10154

+
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