[English] 日本語
Yorodumi
- PDB-9ir1: Crystal structure of CTB10-M40BpA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ir1
TitleCrystal structure of CTB10-M40BpA
ComponentsCTB10
KeywordsBIOSYNTHETIC PROTEIN / artificial photoenzyme
Function / homologyEthD domain / EthD domain / Dimeric alpha-beta barrel / oxidoreductase activity / DI(HYDROXYETHYL)ETHER / CTB10
Function and homology information
Biological speciesCercospora sp. JNU001 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsFu, K. / Rao, Y.J.
Funding support China, 4items
OrganizationGrant numberCountry
Other private2021YFC2102700 China
Other privateBK20202002 China
Other privateKYCX20_1812 China
Other privateKYCX20_1816 China
CitationJournal: To Be Published
Title: Crystal structure of CTB10-M40BpA
Authors: Fu, K. / Rao, Y.J.
History
DepositionJul 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CTB10
B: CTB10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4024
Polymers33,2002
Non-polymers2022
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-39 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.326, 65.581, 49.183
Angle α, β, γ (deg.)90.00, 94.15, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CTB10


Mass: 16599.785 Da / Num. of mol.: 2 / Mutation: M40F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora sp. JNU001 (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A977K7H6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 2.0 M Ammonium sulfate, 2%(W/V) PEG 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→39.28 Å / Num. obs: 23307 / % possible obs: 94.62 % / Redundancy: 6.6 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Net I/σ(I): 13.51
Reflection shellResolution: 1.771→1.834 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.18 / Num. unique obs: 1844 / CC1/2: 0.922 / CC star: 0.98 / Rpim(I) all: 0.165 / Rrim(I) all: 0.407 / % possible all: 76.17

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9IKU

9iku


Resolution: 1.77→39.28 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1088 4.72 %
Rwork0.1839 --
obs0.1858 23044 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 12 177 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062152
X-RAY DIFFRACTIONf_angle_d0.9522910
X-RAY DIFFRACTIONf_dihedral_angle_d7.349305
X-RAY DIFFRACTIONf_chiral_restr0.059311
X-RAY DIFFRACTIONf_plane_restr0.007369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.850.27341150.23712239X-RAY DIFFRACTION78
1.85-1.950.27341390.21692554X-RAY DIFFRACTION89
1.95-2.070.22941540.18762766X-RAY DIFFRACTION96
2.07-2.230.23671390.19362857X-RAY DIFFRACTION99
2.23-2.460.26761280.19432866X-RAY DIFFRACTION98
2.46-2.810.21931420.19652870X-RAY DIFFRACTION99
2.81-3.540.22161380.18032882X-RAY DIFFRACTION99
3.54-39.280.19441330.16042922X-RAY DIFFRACTION99

+
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