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- PDB-9q86: McCP in complex with photocaged nitric oxide, 1.44 s, 9.5 microjo... -

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Basic information

Entry
Database: PDB / ID: 9q86
TitleMcCP in complex with photocaged nitric oxide, 1.44 s, 9.5 microjoule, SSX
ComponentsCytochrome c
KeywordsMETAL BINDING PROTEIN / McCP / heme / gas binding / NO
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 / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionFeb 22, 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: Cytochrome c
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1698
Polymers34,7412
Non-polymers1,4286
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-101 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.183, 107.183, 107.183
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.: 2 / 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.: 51 / 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: 2.95 Å3/Da / Density % sol: 58.36 % / 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
ReflectionResolution: 2→75.91 Å / Num. obs: 28000 / % possible obs: 100 % / Redundancy: 63 % / CC1/2: 0.992 / R split: 0.122 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 48.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1378 / CC1/2: 0.366 / R split: 1.042 / % 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: 6005

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Processing

Software
NameVersionClassification
DIALS3data reduction
xia2data reduction
xia2data scaling
REFMACphasing
Coot0.9.8model building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→75.905 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.502 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.116 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1942 1332 4.757 %
Rwork0.1617 26668 -
all0.163 --
obs-28000 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: 37.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→75.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 92 51 2287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122348
X-RAY DIFFRACTIONr_angle_refined_deg2.4941.8923197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.006516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13810351
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.75110116
X-RAY DIFFRACTIONr_chiral_restr0.1220.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021904
X-RAY DIFFRACTIONr_nbd_refined0.210.2901
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2113
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.23
X-RAY DIFFRACTIONr_mcbond_it3.3473.391108
X-RAY DIFFRACTIONr_mcangle_it4.4876.0531386
X-RAY DIFFRACTIONr_scbond_it5.8263.8321240
X-RAY DIFFRACTIONr_scangle_it8.8896.7611811
X-RAY DIFFRACTIONr_lrange_it9.72436.1483418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2-2.0520.336790.32819790.32820580.8980.9050.33
2.052-2.1080.333890.30419070.30619960.9090.9270.305
2.108-2.1690.2881040.28318130.28419170.9520.940.282
2.169-2.2360.292980.25818020.2619000.9430.950.252
2.236-2.3090.245880.2417210.24118090.9550.9590.228
2.309-2.390.234790.22616930.22717720.9580.9640.21
2.39-2.480.266880.21516330.21817210.960.9690.195
2.48-2.5810.258640.20415840.20616480.9550.9720.181
2.581-2.6960.238680.16815240.17115920.9660.9810.146
2.696-2.8270.195800.1614400.16215200.9770.9830.138
2.827-2.980.215990.16213400.16614390.9730.9840.139
2.98-3.1610.175470.14913330.1513800.9820.9860.128
3.161-3.3780.157630.12812120.12912750.9840.990.111
3.378-3.6490.18550.12711540.1312090.9790.990.115
3.649-3.9960.173500.11710670.11911170.9850.9910.104
3.996-4.4660.152440.0989710.110150.9870.9940.091
4.466-5.1540.114560.0998390.18950.990.9940.093
5.154-6.3050.145340.1237410.1247750.9880.9910.11
6.305-8.8860.173340.1385680.146020.9830.9890.126
8.886-75.9050.159130.183470.183600.9930.9830.18

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