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- PDB-9hyv: DtpB in complex with photocaged nitric oxide, 100 microsecond, 10... -

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Basic information

Entry
Database: PDB / ID: 9hyv
TitleDtpB in complex with photocaged nitric oxide, 100 microsecond, 100 microjoule, SFX
ComponentsDyp-type peroxidase family
KeywordsOXIDOREDUCTASE / peroxidase / DyP / photocage
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / Dyp-type peroxidase family
Function and homology information
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsSmyth, P. / Williams, L.J. / Hough, M.A. / Worrall, J.A.R. / Owen, R.L.
Funding support1items
OrganizationGrant numberCountry
Other government
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 10, 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: 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)209,00818
Polymers205,0336
Non-polymers3,97512
Water16,880937
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23340 Å2
ΔGint-207 kcal/mol
Surface area66260 Å2
Unit cell
Length a, b, c (Å)87.491, 124.436, 193.559
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: 34172.223 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 (E. coli) / References: UniProt: A0ABF7PHP1
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 50 mM HEPES pH 7.5, 150 mM Magnesium chloride, 20% PEG 4000

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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: 1.67→104.64 Å / Num. obs: 241930 / % possible obs: 99.6 % / Redundancy: 47.3 % / CC1/2: 0.989 / Net I/σ(I): 14.2
Reflection shellResolution: 1.67→1.7 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9905 / CC1/2: 0.235

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→45.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.538 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24417 2043 0.8 %RANDOM
Rwork0.21575 ---
obs0.21598 241930 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0 Å2
2--0.2 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.67→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13928 0 270 937 15135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01214721
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613529
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.85420106
X-RAY DIFFRACTIONr_angle_other_deg0.6321.7631076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71651867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2835141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.108102218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.22190
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217960
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023496
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_it2.3212.1197413
X-RAY DIFFRACTIONr_mcbond_other2.3192.1197413
X-RAY DIFFRACTIONr_mcangle_it3.5013.7979289
X-RAY DIFFRACTIONr_mcangle_other3.5013.7979290
X-RAY DIFFRACTIONr_scbond_it3.4492.4977308
X-RAY DIFFRACTIONr_scbond_other3.452.4987302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4824.39610815
X-RAY DIFFRACTIONr_long_range_B_refined7.18320.7316073
X-RAY DIFFRACTIONr_long_range_B_other7.16220.515946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 142 -
Rwork0.35 17749 -
obs--99.99 %

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