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- PDB-7ead: Crystal structure of beta-sheet cytochrome c prime from Thermus t... -

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Entry
Database: PDB / ID: 7ead
TitleCrystal structure of beta-sheet cytochrome c prime from Thermus thermophilus.
ComponentsCytochrome_P460 domain-containing protein
KeywordsELECTRON TRANSPORT / Cytochrome c / thermophile
Function / homologyHEME C / :
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsYoshimi, T. / Fujii, S. / Oki, H. / Igawa, T. / Adams, R.H. / Ueda, K. / Kawahara, K. / Ohkubo, T. / Hough, A.M. / Sambongi, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)26240045 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K07692 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)1617PD0536 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of thermally stable homodimeric cytochrome c'-beta from Thermus thermophilus.
Authors: Yoshimi, T. / Fujii, S. / Oki, H. / Igawa, T. / Adams, H.R. / Ueda, K. / Kawahara, K. / Ohkubo, T. / Hough, M.A. / Sambongi, Y.
History
DepositionMar 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome_P460 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5612
Polymers14,9421
Non-polymers6191
Water2,270126
1
A: Cytochrome_P460 domain-containing protein
hetero molecules

A: Cytochrome_P460 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1214
Polymers29,8842
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4770 Å2
ΔGint-47 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.830, 81.225, 82.305
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

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Components

#1: Protein Cytochrome_P460 domain-containing protein


Mass: 14942.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHC11_22770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A510IM14
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer (pH 7.5) and 20% (w/v) polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→41.15 Å / Num. obs: 13755 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.197 / Net I/σ(I): 11.3 / Num. measured all: 178741 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.74-1.7713.61.314100147390.9022.1100
9.04-41.159.20.05311361230.99835.799.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
PHENIX1.19.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HIH

6hih


Resolution: 1.74→36.42 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 1382 10.09 %
Rwork0.1871 12317 -
obs0.1894 13699 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.19 Å2 / Biso mean: 22.4242 Å2 / Biso min: 12.24 Å2
Refinement stepCycle: final / Resolution: 1.74→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 43 126 1227
Biso mean--16.22 30.57 -
Num. residues----135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.80.38461310.28951199133099
1.8-1.870.31571340.25681218135299
1.87-1.960.30431370.219812121349100
1.96-2.060.26131410.21771196133799
2.06-2.190.26961360.211512221358100
2.19-2.360.23841420.190612231365100
2.36-2.60.2061360.204612311367100
2.6-2.970.21061230.182912581381100
2.98-3.750.15091520.167712521404100
3.75-36.420.16461500.146713061456100

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