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- PDB-9hu1: SSX structure of cytochrome c prime beta from Methylococcus capsu... -

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Basic information

Entry
Database: PDB / ID: 9hu1
TitleSSX structure of cytochrome c prime beta from Methylococcus capsulatus (Bath)
ComponentsCytochrome c
KeywordsMETAL BINDING PROTEIN / McCP / heme / gas binding
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / Cytochrome c
Function and homology information
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 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 20, 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)32,0448
Polymers30,4882
Non-polymers1,5566
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.227, 107.227, 107.227
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

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Components

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Protein , 1 types, 2 molecules BA

#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

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Non-polymers , 5 types, 86 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.96 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: 0.62 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: May 17, 2023
RadiationMonochromator: Cryocooled double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 2.15→75.82 Å / Num. obs: 22647 / % possible obs: 100 % / Redundancy: 69.9 % / CC1/2: 0.984 / R split: 0.188 / Net I/σ(I): 12.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 58.1 % / Num. unique obs: 1156 / CC1/2: 0.279 / R split: 1.017 / % possible all: 100
Serial crystallography measurementCollimation: Kirkpatrick-Baez mirrors / Source size: 300 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
Serial crystallography data reductionFrames total: 25600 / Lattices indexed: 6692

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
DIALSdata reduction
xia2data reduction
xia2data scaling
MOLREPphasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.151→61.984 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.155 / Average fsc free: 0.9458 / Average fsc work: 0.9587 / Cross valid method: FREE R-VALUE / ESU R: 0.188 / ESU R Free: 0.171 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2371 1097 4.845 %
Rwork0.1962 21544 -
all0.198 --
obs-22641 99.996 %
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: 39.596 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.151→61.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 99 80 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122342
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.8893198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6235279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.535532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48410334
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.85610118
X-RAY DIFFRACTIONr_chiral_restr0.0860.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211940
X-RAY DIFFRACTIONr_nbd_refined0.2180.2892
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2129
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3030.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.25
X-RAY DIFFRACTIONr_mcbond_it2.8673.6721110
X-RAY DIFFRACTIONr_mcangle_it4.1476.5871391
X-RAY DIFFRACTIONr_scbond_it3.9054.0661232
X-RAY DIFFRACTIONr_scangle_it6.1337.2751807
X-RAY DIFFRACTIONr_lrange_it9.01440.3973378
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
2.151-2.2060.34940.33515810.33616750.9140.9130.33
2.206-2.2670.326720.31715440.31716160.9170.9270.305
2.267-2.3320.366800.28914990.29215790.9070.9380.276
2.332-2.4040.266740.27914150.27914890.9490.9440.263
2.404-2.4830.293810.27113960.27214770.9350.9460.25
2.483-2.570.334590.25813810.26114400.9130.950.236
2.57-2.6670.25610.2413260.24113870.9580.960.214
2.667-2.7750.298500.21812740.22113240.9440.9660.189
2.775-2.8980.283620.22712250.2312870.9490.9650.196
2.898-3.040.265670.21611530.21912200.9520.9660.183
3.04-3.2040.273670.20111020.20511690.9450.9710.166
3.204-3.3970.2440.15610480.15810920.9740.9830.128
3.397-3.6310.16640.1619810.16110450.9830.9820.138
3.631-3.9210.206510.1559230.1579740.9760.9840.128
3.921-4.2930.208480.1378610.1419090.9760.9870.114
4.293-4.7970.192370.137760.1338130.9770.9890.111
4.797-5.5340.119280.1396950.1387230.9890.9870.116
5.534-6.7640.209260.175950.1716210.9690.980.14
6.764-9.5090.251180.1714820.1745000.9580.980.145
9.509-61.9840.273140.2392870.243010.9340.9620.201

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