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- PDB-9hl1: DtpB in complex with photocaged nitric oxide, 10 ms, 10 microjoul... -

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Basic information

Entry
Database: PDB / ID: 9hl1
TitleDtpB in complex with photocaged nitric oxide, 10 ms, 10 microjoule, SFX
ComponentsDyp-type peroxidase family
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 / Dyp-type peroxidase family
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.56 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
DepositionDec 4, 2024Deposition 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: Dyp-type peroxidase family
B: Dyp-type peroxidase family
C: Dyp-type peroxidase family
D: Dyp-type peroxidase family
E: Dyp-type peroxidase family
F: Dyp-type peroxidase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,82218
Polymers198,9436
Non-polymers3,87912
Water19,8531102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23510 Å2
ΔGint-228 kcal/mol
Surface area66010 Å2
Unit cell
Length a, b, c (Å)87.073, 122.875, 194.936
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
Dyp-type peroxidase family


Mass: 33157.098 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SSPG_00656 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / 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.: 1102 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 291 K / Method: batch mode
Details: 50 mM HEPES pH 7.5, 150 mM Magnesium chloride, 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.127 Å
DetectorType: RAYONIX MX-300 / 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: 1.56→103.95 Å / Num. obs: 295889 / % possible obs: 100 % / Redundancy: 168.6 % / CC1/2: 0.994 / R split: 0.096 / Net I/σ(I): 18.1
Reflection shellResolution: 1.56→1.59 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 14630 / CC1/2: 0.316 / R split: 1.256
Serial crystallography measurementPulse duration: 10 fsec. / Pulse energy: 432 µJ / Pulse photon energy: 10.993 keV / XFEL pulse repetition rate: 30000 Hz
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→44.68 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.767 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23363 2027 0.7 %RANDOM
Rwork0.20874 ---
obs0.20891 293539 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: 23.355 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0 Å2
2--0.14 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.56→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13944 0 270 1102 15316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01214748
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613549
X-RAY DIFFRACTIONr_angle_refined_deg1.981.85420149
X-RAY DIFFRACTIONr_angle_other_deg0.7031.75931130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43151875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.515140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.268102222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.22197
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217997
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023491
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_it2.4182.0537445
X-RAY DIFFRACTIONr_mcbond_other2.4172.0537445
X-RAY DIFFRACTIONr_mcangle_it3.5453.6739337
X-RAY DIFFRACTIONr_mcangle_other3.5453.6749338
X-RAY DIFFRACTIONr_scbond_it3.8482.4547303
X-RAY DIFFRACTIONr_scbond_other3.8372.4547297
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9454.29910813
X-RAY DIFFRACTIONr_long_range_B_refined7.50919.9316208
X-RAY DIFFRACTIONr_long_range_B_other7.46819.4716035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 156 -
Rwork0.377 21493 -
obs--100 %

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