[English] 日本語
Yorodumi
- PDB-5xmo: X-ray crystal structure of Pseudoazurin Met16Phe/Thr36Lys variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xmo
TitleX-ray crystal structure of Pseudoazurin Met16Phe/Thr36Lys variant
ComponentsPseudoazurin
KeywordsELECTRON TRANSPORT / Electron transfer / Cupredoxin
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: 1.19 Å
AuthorsYamaguchi, T. / Kohzuma, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science22550145 Japan
CitationJournal: Photon Factory Activity Report / Year: 2017
Title: X-ray Crystallographic Analysis of M16F/T36K Double Mutant of Pseudoazurin
Authors: Yamaguchi, T. / Takebayashi, N. / Akao, K. / Sakai, C. / Kohzuma, T.
History
DepositionMay 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1412
Polymers13,0771
Non-polymers641
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6380 Å2
Unit cell
Length a, b, c (Å)93.170, 41.160, 34.830
Angle α, β, γ (deg.)90.00, 98.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

-
Components

#1: Protein Pseudoazurin / Blue copper protein


Mass: 13076.994 Da / Num. of mol.: 1 / Mutation: M16F, T36K
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Buffer for crystallization: 0.1 M sodium acetate pH 4.5 Precipitant: 30 % PEG1500 Soaking (Cryoprotectant): 0.1 M Tris-HCl pH 7.5, 40 % PEG1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.192→46.048 Å / Num. obs: 38384 / % possible obs: 92.3 % / Redundancy: 5.4 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.079 / Rsym value: 0.072 / Net I/av σ(I): 6.8 / Net I/σ(I): 12.5
Reflection shellResolution: 1.192→1.223 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.4 / % possible all: 87.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.517
Highest resolutionLowest resolution
Rotation24.61 Å1.33 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALA3.3.22data scaling
iMOSFLM7.2.1data processing
PDB_EXTRACT3.22data extraction
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQK

1bqk


Resolution: 1.19→46.05 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.157 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16116 1936 5 %RANDOM
Rwork0.12792 ---
obs0.12965 36446 92.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.19→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 1 208 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191020
X-RAY DIFFRACTIONr_bond_other_d0.0040.02981
X-RAY DIFFRACTIONr_angle_refined_deg2.7711.9731387
X-RAY DIFFRACTIONr_angle_other_deg1.25632303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74526.21637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69415183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.716151
X-RAY DIFFRACTIONr_chiral_restr0.1920.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211184
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02185
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_it1.4930.956540
X-RAY DIFFRACTIONr_mcbond_other1.4350.954539
X-RAY DIFFRACTIONr_mcangle_it1.8641.444689
X-RAY DIFFRACTIONr_mcangle_other1.9031.446690
X-RAY DIFFRACTIONr_scbond_it2.961.28480
X-RAY DIFFRACTIONr_scbond_other2.9651.276477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1581.774697
X-RAY DIFFRACTIONr_long_range_B_refined4.6915.1181205
X-RAY DIFFRACTIONr_long_range_B_other3.20113.2491136
X-RAY DIFFRACTIONr_rigid_bond_restr5.94232001
X-RAY DIFFRACTIONr_sphericity_free30.9955142
X-RAY DIFFRACTIONr_sphericity_bonded9.29652077
LS refinement shellResolution: 1.192→1.223 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 148 -
Rwork0.193 2534 -
obs--87.3 %

+
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