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- PDB-9hqt: SFX structure of cytochrome c prime beta from Methylococcus capsu... -

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Basic information

Entry
Database: PDB / ID: 9hqt
TitleSFX 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 / FREE ELECTRON LASER / 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 17, 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)36,3899
Polymers34,7412
Non-polymers1,6487
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-96 kcal/mol
Surface area12630 Å2
Unit cell
Length a, b, c (Å)107.1, 107.1, 107.1
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-355-

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) / Strain (production host): BL21(DE3) / Variant (production host): pUC86 / References: UniProt: G1UBD5

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Non-polymers , 5 types, 116 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.95 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: 1.127 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 26, 2019 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.8→33.89 Å / Num. obs: 38160 / % possible obs: 100 % / Redundancy: 233.7 % / CC1/2: 0.938 / R split: 0.204 / Net I/σ(I): 4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 159.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3121 / CC1/2: 0.639 / R split: 0.492 / % possible all: 100
Serial crystallography measurementCollection time total: 0.8 hours / Focal spot size: 2.56 µm2 / Pulse duration: 10 fsec. / Pulse energy: 269.5 µJ / Pulse photon energy: 11 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Oxford silicon chips / Motion control: Geobrick and Smaract / Sample dehydration prevention: 12 um Mylar
Serial crystallography data reductionFrames total: 102400 / Lattices indexed: 14394

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Processing

Software
NameVersionClassification
CrystFELdata reduction
PRIMEdata scaling
MOLREPphasing
REFMAC5.8.0425refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.511 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.219 1886 4.944 %
Rwork0.19 36261 -
all0.191 --
obs-38147 99.945 %
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: 29.718 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 105 109 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122391
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162091
X-RAY DIFFRACTIONr_angle_refined_deg2.3171.8863270
X-RAY DIFFRACTIONr_angle_other_deg0.6281.7954810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.572516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12410342
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.03110116
X-RAY DIFFRACTIONr_chiral_restr0.0870.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022949
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02599
X-RAY DIFFRACTIONr_nbd_refined0.2040.2370
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21843
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21115
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2117
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.212
X-RAY DIFFRACTIONr_nbd_other0.1950.218
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.24
X-RAY DIFFRACTIONr_mcbond_it1.6111.6511135
X-RAY DIFFRACTIONr_mcbond_other1.6111.6521135
X-RAY DIFFRACTIONr_mcangle_it2.3072.9541431
X-RAY DIFFRACTIONr_mcangle_other2.3092.9561432
X-RAY DIFFRACTIONr_scbond_it3.1232.0531256
X-RAY DIFFRACTIONr_scbond_other3.1242.0531255
X-RAY DIFFRACTIONr_scangle_it4.8253.61839
X-RAY DIFFRACTIONr_scangle_other4.8233.61840
X-RAY DIFFRACTIONr_lrange_it7.43417.4662639
X-RAY DIFFRACTIONr_lrange_other7.40117.4232633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3491280.3532698X-RAY DIFFRACTION100
1.847-1.8970.3591080.32557X-RAY DIFFRACTION100
1.897-1.9520.2791300.2552524X-RAY DIFFRACTION100
1.952-2.0120.2161170.2122439X-RAY DIFFRACTION100
2.012-2.0770.2271360.1912376X-RAY DIFFRACTION100
2.077-2.150.2071180.1892280X-RAY DIFFRACTION100
2.15-2.2310.221520.1762215X-RAY DIFFRACTION100
2.231-2.3220.2111150.1652111X-RAY DIFFRACTION100
2.322-2.4240.2011020.1662037X-RAY DIFFRACTION100
2.424-2.5420.1911050.1621964X-RAY DIFFRACTION100
2.542-2.6790.191800.1541889X-RAY DIFFRACTION100
2.679-2.840.185880.1591758X-RAY DIFFRACTION100
2.84-3.0350.197950.1741682X-RAY DIFFRACTION100
3.035-3.2760.217950.1761539X-RAY DIFFRACTION100
3.276-3.5850.165850.1641444X-RAY DIFFRACTION100
3.585-4.0020.196630.1541305X-RAY DIFFRACTION100
4.002-4.6110.196660.1531165X-RAY DIFFRACTION100
4.611-5.6210.202410.181009X-RAY DIFFRACTION100
5.621-7.8420.324340.238794X-RAY DIFFRACTION100
7.842-33.890.543280.599475X-RAY DIFFRACTION97.4806
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.80510.1968-0.21552.4364-0.98452.6039-0.0429-0.1755-0.17640.0849-0.0162-0.03060.12860.14710.05910.02440.00580.02850.0315-0.00130.076231.3242-12.4199-4.9305
23.2177-0.41010.59071.7915-0.14242.06560.03110.1679-0.0143-0.2057-0.04060.0856-0.1493-0.11870.00950.04960.00570.00740.0297-0.01880.03217.62923.8318-19.0636
Refinement TLS groupSelection: ALL

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