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- PDB-9i4u: DtpB in complex with photocaged nitric oxide, 1.24 s, 32.2 microj... -

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Basic information

Entry
Database: PDB / ID: 9i4u
TitleDtpB in complex with photocaged nitric oxide, 1.24 s, 32.2 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
DepositionJan 26, 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
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
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23790 Å2
ΔGint-249 kcal/mol
Surface area66970 Å2
Unit cell
Length a, b, c (Å)86.67, 121.376, 198.163
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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.: 497 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
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.

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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 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→76.873 Å / Num. obs: 82452 / % possible obs: 100 % / Redundancy: 34.1 % / CC1/2: 0.968 / R split: 0.17 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 25.3 % / Num. unique obs: 4038 / CC1/2: 0.585 / R split: 0.589 / % possible all: 100
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: 5536

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6yrj

6yrj


Resolution: 2.4→76.873 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.147 / SU B: 8.41 / SU ML: 0.188 / Average fsc free: 0.9585 / Average fsc work: 0.9717 / Cross valid method: FREE R-VALUE / ESU R: 0.4 / ESU R Free: 0.237 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2225 4160 5.045 %
Rwork0.1822 78292 -
all0.184 --
obs-82452 99.995 %
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: 34.668 Å2
Baniso -1Baniso -2Baniso -3
1--0.088 Å2-0 Å20 Å2
2--0.237 Å2-0 Å2
3----0.148 Å2
Refinement stepCycle: LAST / Resolution: 2.4→76.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13982 0 270 497 14749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01214814
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.85720212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93251872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.9895143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.222102241
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.98810682
X-RAY DIFFRACTIONr_chiral_restr0.0760.22193
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211570
X-RAY DIFFRACTIONr_nbd_refined0.170.26019
X-RAY DIFFRACTIONr_nbtor_refined0.2930.210052
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2695
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.26
X-RAY DIFFRACTIONr_mcbond_it1.3153.3987448
X-RAY DIFFRACTIONr_mcangle_it2.3856.1059328
X-RAY DIFFRACTIONr_scbond_it1.4873.4987366
X-RAY DIFFRACTIONr_scangle_it2.6256.38510884
X-RAY DIFFRACTIONr_lrange_it4.80233.08421196
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
2.4-2.4620.2933050.26856830.26959880.9410.951000.24
2.462-2.530.3172970.27255980.27558950.9160.9481000.241
2.53-2.6030.2952800.24553990.24756790.9440.961000.212
2.603-2.6830.2892710.23852890.24155600.9430.9631000.205
2.683-2.7710.2672780.22851240.2354020.9540.9661000.195
2.771-2.8680.2932620.22649460.22952080.9460.9661000.192
2.868-2.9760.252500.21147750.21350250.9590.971000.178
2.976-3.0970.2482670.20246350.20449020.9570.9731000.169
3.097-3.2350.2412220.18944050.19246270.9640.9761000.158
3.235-3.3920.2062190.17542290.17744480.9690.981000.149
3.392-3.5760.2152280.16540300.16742580.970.9821000.136
3.576-3.7920.1851880.15838530.15940410.9770.9841000.133
3.792-4.0530.1781840.14336070.14537910.9820.9871000.121
4.053-4.3770.1681920.13933640.14135570.9830.98899.97190.121
4.377-4.7930.1911690.13531150.13732840.9770.9891000.117
4.793-5.3560.1751470.14128310.14329780.9820.9871000.122
5.356-6.180.2051340.15725250.15926590.9750.9831000.133
6.18-7.5560.1831050.15621570.15722620.9750.9841000.136
7.556-10.6350.1951040.16516950.16717990.9770.9841000.147
10.635-76.8730.306560.27610140.27710700.9520.9661000.253

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