[English] 日本語
Yorodumi
- PDB-9ia9: DtpB in complex with photocaged nitric oxide, 1.24 s, 8.05 microj... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ia9
TitleDtpB in complex with photocaged nitric oxide, 1.24 s, 8.05 microjoule, SSX
ComponentsDyp-type peroxidase family
KeywordsMETAL BINDING PROTEIN / DtpB / heme / gas binding / nitric oxide
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Dyp-type peroxidase family
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSmyth, P. / Williams, L.J. / Hough, M.A. / Worrall, J.A.R. / Owen, R.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: Iucrj / Year: 2025
Title: Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide.
Authors: Smyth, P. / Jaho, S. / Williams, L.J. / Karras, G. / Fitzpatrick, A. / Thompson, A.J. / Battah, S. / Axford, D. / Horrell, S. / Lucic, M. / Ishihara, K. / Kataoka, M. / Matsuura, H. / ...Authors: Smyth, P. / Jaho, S. / Williams, L.J. / Karras, G. / Fitzpatrick, A. / Thompson, A.J. / Battah, S. / Axford, D. / Horrell, S. / Lucic, M. / Ishihara, K. / Kataoka, M. / Matsuura, H. / Shimba, K. / Tono, K. / Tosha, T. / Sugimoto, H. / Owada, S. / Hough, M.A. / Worrall, J.A.R. / Owen, R.L.
History
DepositionFeb 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Dyp-type peroxidase family
A: Dyp-type peroxidase family
B: Dyp-type peroxidase family
C: Dyp-type peroxidase family
D: Dyp-type peroxidase family
E: Dyp-type peroxidase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,93518
Polymers214,0566
Non-polymers3,87912
Water8,233457
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24350 Å2
ΔGint-233 kcal/mol
Surface area66310 Å2
Unit cell
Length a, b, c (Å)87.101, 122.913, 195.038
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Dyp-type peroxidase family


Mass: 35675.941 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SSPG_00656 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U8UU09
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Description: Crystals 10 x 8 um grew at room temperature within 24-48 h.
Crystal growTemperature: 291 K / Method: batch mode
Details: 6-10 mg/ml of protein in 50 mm sodium acetate, 150 mm NaCl pH 5 mixed with 150 mM MgCl2, 150 mm HEPES, 20 % PEG 4000, pH 7.5.

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→79.66 Å / Num. obs: 82535 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 0.958 / R split: 0.197 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4074 / CC1/2: 0.379 / R split: 0.819
Serial crystallography measurementCollimation: Kirkpatrick-Baez mirrors / Source size: 300 µm2
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Oxford silicon chip / Motion control: Geobrick and Smaract / Sample dehydration prevention: 12 um EVAL and 6 um Mylar
Serial crystallography data reductionFrames total: 25600 / Lattices indexed: 3109

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→79.657 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.173 / WRfactor Rwork: 0.137 / SU B: 9.07 / SU ML: 0.195 / Average fsc free: 0.9569 / Average fsc work: 0.97 / Cross valid method: FREE R-VALUE / ESU R: 0.395 / ESU R Free: 0.235 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2196 4175 5.06 %
Rwork0.1769 78329 -
all0.179 --
obs-82504 99.885 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.069 Å20 Å2-0 Å2
2--0.451 Å20 Å2
3----0.382 Å2
Refinement stepCycle: LAST / Resolution: 2.4→79.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13978 0 270 457 14705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01215007
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.85720495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95851910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.3775151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.868102286
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.98510692
X-RAY DIFFRACTIONr_chiral_restr0.080.22216
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211768
X-RAY DIFFRACTIONr_nbd_refined0.1740.26038
X-RAY DIFFRACTIONr_nbtor_refined0.2940.210131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2672
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.070.29
X-RAY DIFFRACTIONr_mcbond_it1.3463.6937548
X-RAY DIFFRACTIONr_mcangle_it2.4296.6359483
X-RAY DIFFRACTIONr_scbond_it1.5993.7797459
X-RAY DIFFRACTIONr_scangle_it2.7856.9111012
X-RAY DIFFRACTIONr_lrange_it4.65135.98221395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.3492830.27957470.28260360.9120.94299.90060.254
2.462-2.530.2962950.26455700.26558730.940.9599.86380.236
2.53-2.6030.3222920.2654190.26357240.930.95399.77290.229
2.603-2.6830.2792780.25752620.25955450.9450.95499.90980.223
2.683-2.7710.2892730.24551070.24753910.9410.9699.7960.209
2.771-2.8680.3122820.2449280.24452190.940.9699.82760.205
2.868-2.9760.2682280.21648040.21950380.9510.96899.88090.182
2.976-3.0970.2422340.20146390.20348760.960.97299.93850.166
3.097-3.2350.262460.19944390.20246910.9570.97399.87210.167
3.235-3.3930.2222360.17542250.17744630.9680.9899.95520.145
3.393-3.5760.2272210.16440150.16742420.9690.98299.85860.137
3.576-3.7920.1942250.14938310.15240610.9770.98599.87690.125
3.792-4.0530.1681990.13335660.13537720.9820.98999.81440.109
4.053-4.3770.1731630.13534050.13735720.9820.98999.8880.111
4.377-4.7930.1581830.12330960.12532800.9850.99199.96950.103
4.793-5.3570.1631530.1328520.13130050.9850.991000.107
5.357-6.1810.1771260.14325170.14426430.9820.9871000.117
6.181-7.5590.1731100.13321610.13522720.9820.98899.9560.109
7.559-10.6420.1551020.12316920.12417940.9890.9911000.105
10.642-79.6570.221450.21310330.21310780.9770.9741000.186

+
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