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- PDB-9htt: McCP in complex with photocaged nitric oxide, 1.44 s, 0.19 microj... -

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Basic information

Entry
Database: PDB / ID: 9htt
TitleMcCP in complex with photocaged nitric oxide, 1.44 s, 0.19 microjoule, SSX
ComponentsCytochrome c
KeywordsMETAL BINDING PROTEIN / McCP / heme / gas binding
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / NITRIC OXIDE / Cytochrome c
Function and homology information
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.75 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
DepositionDec 19, 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

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1047
Polymers34,7412
Non-polymers1,3625
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-72 kcal/mol
Surface area12960 Å2
Unit cell
Length a, b, c (Å)107.321, 107.321, 107.321
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

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Components

#1: Protein Cytochrome c


Mass: 17370.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus str. Bath (bacteria)
Gene: ccp, MCA2394 / Plasmid: pBluescript SK(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pUC86 / References: UniProt: G1UBD5
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 63.6 % / Description: Cubes of approx 30 um grew within 24 h.
Crystal growTemperature: 291 K / Method: batch mode
Details: Final concentrations: 20 mg/mL protein, 50 mM HEPES pH 7.5, 34 % (v/v) polyethylene glycol 550, 500 mM MES pH 6.5, 5 mM ZnSO4.

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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: Sep 30, 2021
RadiationMonochromator: Cryocooled double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.4869
pseudo-merohedral22L, -K, H20.5131
ReflectionResolution: 1.75→75.89 Å / Num. obs: 41713 / % possible obs: 100 % / Redundancy: 121.2 % / CC1/2: 0.997 / R split: 0.076 / Net I/σ(I): 8.2
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2043 / CC1/2: 0.294 / R split: 1.27 / % possible all: 100
Serial crystallography measurementCollection time total: 0.3 hours / Collimation: Kirkpatrick-Baez mirrors / Source size: 64 µm2
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Oxford silicon chip / Motion control: Geobrick and Smaract / Sample dehydration prevention: 6 um Mylar, 6 um EVAL
Serial crystallography data reductionFrames total: 25600 / Lattices indexed: 17766

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Processing

Software
NameVersionClassification
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.75→75.89 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.878 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.086 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1994 2034 4.876 %
Rwork0.1666 39679 -
all0.168 --
obs-41713 100 %
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: 34.204 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→75.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 91 64 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122355
X-RAY DIFFRACTIONr_angle_refined_deg2.5281.8913210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.934516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14810352
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.30710116
X-RAY DIFFRACTIONr_chiral_restr0.1420.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021912
X-RAY DIFFRACTIONr_nbd_refined0.2030.2850
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2106
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0430.24
X-RAY DIFFRACTIONr_mcbond_it3.5193.0291112
X-RAY DIFFRACTIONr_mcangle_it4.5485.41392
X-RAY DIFFRACTIONr_scbond_it5.7083.5531243
X-RAY DIFFRACTIONr_scangle_it8.7546.231816
X-RAY DIFFRACTIONr_lrange_it9.67631.9363368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7960.3721590.3762857X-RAY DIFFRACTION100
1.796-1.8450.3361480.3522850X-RAY DIFFRACTION100
1.845-1.8980.3081510.312743X-RAY DIFFRACTION100
1.898-1.9570.2671190.2692707X-RAY DIFFRACTION100
1.957-2.0210.271320.2312607X-RAY DIFFRACTION100
2.021-2.0920.261040.212525X-RAY DIFFRACTION100
2.092-2.1710.2351320.1992418X-RAY DIFFRACTION100
2.171-2.2590.218980.1932369X-RAY DIFFRACTION100
2.259-2.3590.2251150.182242X-RAY DIFFRACTION100
2.359-2.4750.21270.1792145X-RAY DIFFRACTION100
2.475-2.6080.204960.1622040X-RAY DIFFRACTION100
2.608-2.7660.191230.1541921X-RAY DIFFRACTION100
2.766-2.9570.214950.161814X-RAY DIFFRACTION100
2.957-3.1930.196890.151718X-RAY DIFFRACTION100
3.193-3.4980.164830.1241559X-RAY DIFFRACTION100
3.498-3.9090.181910.1321432X-RAY DIFFRACTION100
3.909-4.5120.157480.1131287X-RAY DIFFRACTION100
4.512-5.5220.138460.1181086X-RAY DIFFRACTION100
5.522-7.7880.141550.147848X-RAY DIFFRACTION100
7.788-75.890.204230.173511X-RAY DIFFRACTION100

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