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- PDB-9qme: McCP in complex with photocaged nitric oxide, 20 ms, 12.9 microjo... -

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Basic information

Entry
Database: PDB / ID: 9qme
TitleMcCP in complex with photocaged nitric oxide, 20 ms, 12.9 microjoule, SFX
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionMar 23, 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)36,1968
Polymers34,7412
Non-polymers1,4556
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-71 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.766, 107.766, 107.766
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 28 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 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: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.25 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 4, 2022 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5086
pseudo-merohedral22L, -K, H20.4914
ReflectionResolution: 2.25→29.907 Å / Num. obs: 20088 / % possible obs: 100 % / Redundancy: 430.4 % / CC1/2: 0.996 / R split: 0.109 / Net I/σ(I): 6.3
Reflection shellResolution: 2.25→2.29 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1013 / CC1/2: 0.358 / R split: 1.16 / % possible all: 100
Serial crystallography measurementFocal spot size: 2.6 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 9.94 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: SACLA HVE injector / Method: injection
Serial crystallography sample delivery injectionDescription: SACLA HVE injector / Injector diameter: 100 µm / Injector temperature: 300 K
Serial crystallography data reductionFrames total: 79992 / Lattices indexed: 11235 / XFEL run numbers: 113928-113959

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Processing

Software
NameVersionClassification
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Coot0.9.8model building
REFMAC5.8.0430 (refmacat 0.4.100)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→29.907 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.126 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.209 / ESU R Free: 0.177 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2228 1080 5.378 %
Rwork0.1902 19003 -
all0.192 --
obs-20083 99.94 %
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: 50.194 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 97 22 2263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122336
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.8973175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4535274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.848532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74310347
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.58410117
X-RAY DIFFRACTIONr_chiral_restr0.0980.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211916
X-RAY DIFFRACTIONr_nbd_refined0.2220.2796
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.275
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.219
X-RAY DIFFRACTIONr_mcbond_it4.0564.6971098
X-RAY DIFFRACTIONr_mcangle_it5.6738.4351370
X-RAY DIFFRACTIONr_scbond_it6.2315.1771238
X-RAY DIFFRACTIONr_scangle_it9.2939.231805
X-RAY DIFFRACTIONr_lrange_it10.75748.1343203
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
2.25-2.3080.286580.34114200.33914780.9390.9140.344
2.308-2.3710.319960.31813270.31814230.9250.9210.321
2.371-2.4390.372890.29612800.313690.9020.9370.294
2.439-2.5140.314700.27312780.27613480.9340.9430.269
2.514-2.5960.297790.24412190.24712980.940.9570.235
2.596-2.6860.253720.22512050.22712770.9630.9660.21
2.686-2.7870.25620.20911480.21112100.9590.970.192
2.787-2.8990.288720.23111120.23411840.9510.9660.201
2.899-3.0270.227690.18810540.1911230.9690.9780.16
3.027-3.1730.204540.17810620.1811160.9730.980.151
3.173-3.3430.193630.1639510.16510140.9770.9850.143
3.343-3.5430.157450.1439340.1449790.9860.990.132
3.543-3.7830.173310.1498740.159050.980.9870.136
3.783-4.0810.152510.1458310.1458820.9870.9880.129
4.081-4.4620.178350.157690.1518040.9890.9890.135
4.462-4.9750.226290.1556900.1587190.9760.9890.141
4.975-5.7190.204390.1766150.1776540.9760.9840.149
5.719-6.9410.314260.2435380.2465640.9650.9760.205
6.941-9.5610.197200.1984260.1984460.9790.9840.183
9.561-29.9070.226200.2262700.2262900.9730.9760.214

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