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- PDB-9hs8: Cytochrome c prime beta from Methylococcus capsulatus (Bath) in c... -

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Basic information

Entry
Database: PDB / ID: 9hs8
TitleCytochrome c prime beta from Methylococcus capsulatus (Bath) in complex with nitric oxide from proli NONOate
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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 18, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,35310
Polymers34,7412
Non-polymers1,6128
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-99 kcal/mol
Surface area12730 Å2
Unit cell
Length a, b, c (Å)107.441, 107.441, 107.441
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

21A-305-

HOH

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Components

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Protein , 1 types, 2 molecules BA

#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) / Variant (production host): pUC86 / References: UniProt: G1UBD5

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-HEC / HEME C


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.97 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: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationMonochromator: Cryocooled double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.85→76.09 Å / Num. obs: 35508 / % possible obs: 100 % / Redundancy: 175.4 % / CC1/2: 0.998 / R split: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 137.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1741 / CC1/2: 0.534 / R split: 0.936 / % possible all: 100
Serial crystallography measurementCollection time total: 0.15 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: 12 um Mylar
Serial crystallography data reductionFrames total: 25600 / Lattices indexed: 11352

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Processing

Software
NameVersionClassification
DIALSdata reduction
xia2data reduction
MOLREPphasing
Cootmodel building
REFMAC5.8.0425refinement
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→76.088 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.926 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.091 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1795 1729 4.869 %
Rwork0.1551 33778 -
all0.156 --
obs-35507 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: 34.669 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→76.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 104 95 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122446
X-RAY DIFFRACTIONr_angle_refined_deg2.5531.8863340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.589517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06810362
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.33610120
X-RAY DIFFRACTIONr_chiral_restr0.1470.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022000
X-RAY DIFFRACTIONr_nbd_refined0.2080.2899
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2133
X-RAY DIFFRACTIONr_metal_ion_refined0.2450.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.25
X-RAY DIFFRACTIONr_mcbond_it3.6823.1331161
X-RAY DIFFRACTIONr_mcangle_it5.0395.5861468
X-RAY DIFFRACTIONr_scbond_it5.6633.5351285
X-RAY DIFFRACTIONr_scangle_it8.3926.2361872
X-RAY DIFFRACTIONr_lrange_it9.8233.4083516
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
1.85-1.8980.3061360.34124730.33926090.9440.9330.337
1.898-1.950.311430.29323830.29425260.9410.9450.284
1.95-2.0070.261770.24823690.24824460.9550.9590.229
2.007-2.0680.271020.22723130.22924150.9550.9660.204
2.068-2.1360.2451100.22521900.22623000.9590.9670.201
2.136-2.2110.2551260.20221360.20422620.9580.9720.175
2.211-2.2950.25900.19520850.19721750.9590.9760.168
2.295-2.3880.2431070.18919900.19220970.9650.9770.163
2.388-2.4940.2461240.1818670.18419910.9590.980.151
2.494-2.6160.182990.16918270.1719260.9790.9810.14
2.616-2.7570.211890.15217350.15418240.9740.9850.128
2.757-2.9240.18850.14816630.14917480.9790.9860.125
2.924-3.1260.148710.14215510.14216220.9860.9870.121
3.126-3.3760.157730.12214790.12415520.9840.990.106
3.376-3.6970.136680.12113440.12114120.9880.9910.111
3.697-4.1320.122700.10412050.10512750.9910.9930.097
4.132-4.7690.105510.09310760.09311270.9940.9950.091
4.769-5.8350.126470.1119340.1119810.990.9920.106
5.835-8.2280.138340.1447280.1447620.9910.9880.139
8.228-76.0880.229270.1934300.1954570.9710.9810.2

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