[English] 日本語
Yorodumi
- PDB-9hnn: Structure of the (6-4) photolyase of Caulobacter crescentus in it... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hnn
TitleStructure of the (6-4) photolyase of Caulobacter crescentus in its fully reduced state determined by serial femtosecond crystallography
ComponentsCryptochrome/photolyase family protein
KeywordsFLAVOPROTEIN / DNA repair / photolyase / electron transfer / iron-sulfur cluster
Function / homologyPhotolyase PhrB-like / : / Deoxyribodipyrimidine photo-lyase-related protein / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Chem-DLZ / FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Cryptochrome/photolyase family protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsPo Hsun, W. / Maestre-Reyna, M. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ES152/18 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Redox-State-Dependent Structural Changes within a Prokaryotic 6-4 Photolyase.
Authors: Wang, P.H. / Hosokawa, Y. / C Soares, J. / Emmerich, H.J. / Fuchs, V. / Caramello, N. / Engilberge, S. / Bologna, A. / Rosner, C.J. / Nakamura, M. / Watad, M. / Luo, F. / Owada, S. / Tosha, ...Authors: Wang, P.H. / Hosokawa, Y. / C Soares, J. / Emmerich, H.J. / Fuchs, V. / Caramello, N. / Engilberge, S. / Bologna, A. / Rosner, C.J. / Nakamura, M. / Watad, M. / Luo, F. / Owada, S. / Tosha, T. / Kang, J. / Tono, K. / Bessho, Y. / Nango, E. / Pierik, A.J. / Royant, A. / Tsai, M.D. / Yamamoto, J. / Maestre-Reyna, M. / Essen, L.O.
History
DepositionDec 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cryptochrome/photolyase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5854
Polymers58,1211
Non-polymers1,4633
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-27 kcal/mol
Surface area21010 Å2
Unit cell
Length a, b, c (Å)49.800, 103.400, 104.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Cryptochrome/photolyase family protein


Mass: 58121.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: CC_0646 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q9AAF5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine


Mass: 326.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5 / Details: 0.1 M Tris (pH 8.5) 0.2 M MgCl2 20% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.78→24.9 Å / Num. obs: 52730 / % possible obs: 100 % / Redundancy: 843 % / Biso Wilson estimate: 21.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.46
Reflection shellResolution: 1.78→1.84 Å / Rmerge(I) obs: 1.132 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 5187 / CC1/2: 0.544
Serial crystallography sample deliveryDescription: LCP extruder / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: grease / Description: LCP extruder / Power by: HPLC
Preparation: Crystals transferred to carrier solvent under safety light
Serial crystallography data reductionCrystal hits: 63432 / Frames indexed: 46160

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→24.9 Å / SU ML: 0.2491 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.7188
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 2583 4.91 %
Rwork0.1839 50059 -
obs0.1853 52642 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.06 Å2
Refinement stepCycle: LAST / Resolution: 1.78→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 84 266 4428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634334
X-RAY DIFFRACTIONf_angle_d0.96045893
X-RAY DIFFRACTIONf_chiral_restr0.0507600
X-RAY DIFFRACTIONf_plane_restr0.01767
X-RAY DIFFRACTIONf_dihedral_angle_d15.62081596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.46221290.39262732X-RAY DIFFRACTION100
1.81-1.850.3851520.37232757X-RAY DIFFRACTION100
1.85-1.890.40811320.36952725X-RAY DIFFRACTION100
1.89-1.940.4281500.33912730X-RAY DIFFRACTION100
1.94-1.980.34181380.31922770X-RAY DIFFRACTION100
1.98-2.040.32241480.31022720X-RAY DIFFRACTION100
2.04-2.10.34031470.29392761X-RAY DIFFRACTION100
2.1-2.170.27181440.28212785X-RAY DIFFRACTION100
2.17-2.240.25491540.26732715X-RAY DIFFRACTION100
2.24-2.330.27051300.24632774X-RAY DIFFRACTION100
2.33-2.440.24761490.22532760X-RAY DIFFRACTION100
2.44-2.570.26491520.22262758X-RAY DIFFRACTION100
2.57-2.730.26581470.20712799X-RAY DIFFRACTION100
2.73-2.940.2211540.192781X-RAY DIFFRACTION100
2.94-3.230.19131310.16272806X-RAY DIFFRACTION100
3.23-3.70.12511280.12152849X-RAY DIFFRACTION100
3.7-4.660.12221440.09792856X-RAY DIFFRACTION100
4.66-24.90.13031540.09992981X-RAY DIFFRACTION99.78

+
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