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- PDB-9htv: McCP in complex with photocaged nitric oxide, 1.44 s, 0.95 microj... -

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Basic information

Entry
Database: PDB / ID: 9htv
TitleMcCP in complex with photocaged nitric oxide, 1.44 s, 0.95 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: 1.8 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)31,8517
Polymers30,4882
Non-polymers1,3625
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.408, 107.408, 107.408
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: 15244.063 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) / 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.: 68 / 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, L10.7955
pseudo-merohedral22L, -K, H20.2045
ReflectionResolution: 1.8→76.064 Å / Num. obs: 38471 / % possible obs: 100 % / Redundancy: 59.7 % / CC1/2: 0.993 / R split: 0.111 / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 47.1 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1909 / CC1/2: 0.399 / R split: 0.943 / % 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: 7713

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
DIALSdata reduction
PRIMEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→76.064 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.763 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.084 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1815 1997 5.191 %
Rwork0.1613 36474 -
all0.162 --
obs-38471 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: 31.963 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→76.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 91 68 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122351
X-RAY DIFFRACTIONr_angle_refined_deg2.2031.8923201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.748532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02810350
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.42710116
X-RAY DIFFRACTIONr_chiral_restr0.1460.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211932
X-RAY DIFFRACTIONr_nbd_refined0.2070.2834
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21531
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2105
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.22
X-RAY DIFFRACTIONr_mcbond_it3.3592.8251112
X-RAY DIFFRACTIONr_mcangle_it4.6035.0331391
X-RAY DIFFRACTIONr_scbond_it5.6993.3111239
X-RAY DIFFRACTIONr_scangle_it8.7225.781810
X-RAY DIFFRACTIONr_lrange_it9.73530.1873303
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
1.8-1.8470.3261380.33526540.33527920.9410.9240.337
1.847-1.8970.2971460.30926160.30827620.9380.9370.305
1.897-1.9520.2591770.26625020.26526790.9550.9520.258
1.952-2.0130.2841300.24324510.24525810.9460.960.23
2.013-2.0780.2481210.21923720.2224930.9580.9670.203
2.078-2.1510.2071200.21823410.21824610.9710.9680.202
2.151-2.2320.2071420.222100.223520.9720.9740.183
2.232-2.3240.2211140.18721570.18922710.9620.9770.17
2.324-2.4270.18870.1820810.1821680.9820.9790.163
2.427-2.5450.222840.18220230.18421070.9680.9790.164
2.545-2.6830.1831300.15818290.1619590.9780.9840.142
2.683-2.8450.1981120.15617720.15818840.9750.9840.138
2.845-3.0410.184910.1516990.15217900.9790.9850.136
3.041-3.2840.17690.14415730.14516420.9820.9860.132
3.284-3.5970.152800.11414490.11615290.9850.9910.107
3.597-4.0210.127810.11413080.11513890.9880.9920.11
4.021-4.6410.113530.111850.112380.9920.9940.1
4.641-5.6780.123550.1099960.1110510.9910.9930.107
5.678-8.0080.184430.1417900.1438330.9810.9870.138
8.008-76.0640.146240.1654660.1644900.9880.9840.174

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