[English] 日本語
Yorodumi
- PDB-8zyh: Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/H54A/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zyh
TitleCrystal structure of a cupin protein (tm1459, I49C-4py/H52A/H54A/C106D mutant) in copper (Cu) substituted form
ComponentsCupin type-2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Artificial Metalloenzymes / Chemical Modification
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / COPPER (II) ION / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsMorita, Y. / Kubo, H. / Matsumoto, R. / Fujieda, N.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21KK0249 Japan
Japan Society for the Promotion of Science (JSPS)23K13764 Japan
Japan Society for the Promotion of Science (JSPS)JP21H01954 Japan
Japan Society for the Promotion of Science (JSPS)24K01503 Japan
CitationJournal: To Be Published
Title: Copper center in artificial non-heme metalloenzyme
Authors: Morita, Y. / Kubo, H. / Matsumoto, R. / Fujieda, N.
History
DepositionJun 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cupin type-2 domain-containing protein
B: Cupin type-2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2826
Polymers26,8092
Non-polymers4734
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-64 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.570, 58.500, 71.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cupin type-2 domain-containing protein


Mass: 13404.310 Da / Num. of mol.: 2 / Mutation: I49C/H52A/H54A/C106D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1459 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1H0
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 26-28% w/v Jeffamine ED-2001, 0.1M MES pH6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.07→50 Å / Num. obs: 176945 / % possible obs: 98.5 % / Redundancy: 3.32 % / CC1/2: 0.997 / Net I/σ(I): 14.7
Reflection shellResolution: 1.07→1.14 Å / Redundancy: 2.72 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 27751 / CC1/2: 0.806 / % possible all: 95.6

-
Processing

Software
NameClassification
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.163 9819 5 %RANDOM
Rwork0.137 ---
obs0.1385 176945 89.5 %-
Refine analyzeNum. disordered residues: 29
Refinement stepCycle: LAST / Resolution: 1.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8694 0 58 844 9596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.4343
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1543
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.2864
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.1361
X-RAY DIFFRACTIONs_approx_iso_adps0

+
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://pdbjlvh1.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