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- PDB-8brl: Room temperature crystal structure of cytochrome c' from Hydrogen... -

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Basic information

Entry
Database: PDB / ID: 8brl
TitleRoom temperature crystal structure of cytochrome c' from Hydrogenophilus thermoluteolus
ComponentsCytochrome c prime
KeywordsELECTRON TRANSPORT / Heme protein / diatomic gas binding protein / electron transfer
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562
Similarity search - Domain/homology
HEME C / Cytochrome c prime
Similarity search - Component
Biological speciesHydrogenophilus thermoluteolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsFujii, S. / Hough, M.A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
History
DepositionNov 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Cytochrome c prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5643
Polymers14,8491
Non-polymers7152
Water77543
1
D: Cytochrome c prime
hetero molecules

D: Cytochrome c prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1276
Polymers29,6982
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area4460 Å2
ΔGint-75 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.536, 83.536, 88.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11D-308-

HOH

21D-342-

HOH

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Components

#1: Protein Cytochrome c prime


Mass: 14848.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenophilus thermoluteolus (bacteria)
Gene: cytc, HPTL_0021 / Production host: Escherichia coli (E. coli) / References: UniProt: F7J213
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 8000, 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Apr 14, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.88→56.09 Å / Num. obs: 15440 / % possible obs: 100 % / Redundancy: 22.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.459 / Rpim(I) all: 0.093 / Rrim(I) all: 0.469 / Net I/σ(I): 7.9
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 15.4 % / Rmerge(I) obs: 5.496 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 750 / CC1/2: 0.258 / Rpim(I) all: 1.401 / Rrim(I) all: 5.683 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3I

5b3i


Resolution: 1.88→56.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.955 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20314 777 5 %RANDOM
Rwork0.17791 ---
obs0.17918 14620 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.88→56.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 48 43 1120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131100
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161047
X-RAY DIFFRACTIONr_angle_refined_deg2.321.7241492
X-RAY DIFFRACTIONr_angle_other_deg1.4811.6332413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96824.5151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29515197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.823154
X-RAY DIFFRACTIONr_chiral_restr0.1580.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021252
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02244
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7632.855535
X-RAY DIFFRACTIONr_mcbond_other2.7622.842534
X-RAY DIFFRACTIONr_mcangle_it4.1624.257667
X-RAY DIFFRACTIONr_mcangle_other4.1594.273668
X-RAY DIFFRACTIONr_scbond_it5.2473.522565
X-RAY DIFFRACTIONr_scbond_other5.0953.482559
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8734.899819
X-RAY DIFFRACTIONr_long_range_B_refined9.37933.1591312
X-RAY DIFFRACTIONr_long_range_B_other9.3533.0711308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 61 -
Rwork0.357 1039 -
obs--99.1 %

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