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- PDB-9hxx: DtpB in complex with photocaged nitric oxide, 100 microsecond, 30... -

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Basic information

Entry
Database: PDB / ID: 9hxx
TitleDtpB in complex with photocaged nitric oxide, 100 microsecond, 30 microjoule, SFX
ComponentsDye-decolorizing peroxidase (DyP), encapsulated subgroup
KeywordsOXIDOREDUCTASE / Peroxidase / DyP / photocage
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 / Dye-decolorizing peroxidase (DyP), encapsulated subgroup
Similarity search - Component
Biological speciesStreptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.52 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
DepositionJan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dye-decolorizing peroxidase (DyP), encapsulated subgroup
B: Dye-decolorizing peroxidase (DyP), encapsulated subgroup
C: Dye-decolorizing peroxidase (DyP), encapsulated subgroup
D: Dye-decolorizing peroxidase (DyP), encapsulated subgroup
E: Dye-decolorizing peroxidase (DyP), encapsulated subgroup
F: Dye-decolorizing peroxidase (DyP), encapsulated subgroup
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,91218
Polymers205,0336
Non-polymers3,87912
Water19,4201078
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23430 Å2
ΔGint-229 kcal/mol
Surface area66220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.475, 124.392, 193.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Dye-decolorizing peroxidase (DyP), encapsulated subgroup


Mass: 34172.223 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SLI_7409 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9HFU5
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1078 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 50 mM HEPES pH 7.5, 150 mM Magnesium chloride 20% PEG4000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.127 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.52→104.64 Å / Num. obs: 322685 / % possible obs: 100 % / Redundancy: 167 % / CC1/2: 0.996 / Net I/σ(I): 19.4
Reflection shellResolution: 1.52→1.55 Å / Num. unique obs: 15959 / CC1/2: 0.317 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→45.13 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.628 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 2084 0.6 %RANDOM
Rwork0.20899 ---
obs0.20916 320258 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.938 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20 Å2
2--0.14 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.52→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13944 0 278 1078 15300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01214763
X-RAY DIFFRACTIONr_bond_other_d0.0020.01613601
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.85420174
X-RAY DIFFRACTIONr_angle_other_deg0.6831.7631243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21551879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.0845141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.397102232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.22204
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217994
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023494
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_it2.3512.017431
X-RAY DIFFRACTIONr_mcbond_other2.3512.017431
X-RAY DIFFRACTIONr_mcangle_it3.4993.69311
X-RAY DIFFRACTIONr_mcangle_other3.4993.6019312
X-RAY DIFFRACTIONr_scbond_it3.8452.4147332
X-RAY DIFFRACTIONr_scbond_other3.8322.4147326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9024.22510855
X-RAY DIFFRACTIONr_long_range_B_refined7.59919.7616152
X-RAY DIFFRACTIONr_long_range_B_other7.56119.4215988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 158 -
Rwork0.362 23520 -
obs--100 %

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