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- PDB-8brk: Room temperature crystal structure of cytochrome c' from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 8brk
TitleRoom temperature crystal structure of cytochrome c' from Thermus thermophilus
ComponentsProbable cytochrome
KeywordsELECTRON TRANSPORT / Heme protein / diatomic gas binding protein / electron transfer
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / Probable cytochrome
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5612
Polymers14,9421
Non-polymers6191
Water1,35175
1
A: Probable cytochrome
hetero molecules

A: Probable cytochrome
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 operation2_555-x,y,-z1
Buried area4750 Å2
ΔGint-48 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.535, 38.986, 41.525
Angle α, β, γ (deg.)90.00, 97.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable cytochrome


Mass: 14942.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_P0091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q746G4
#2: Chemical ChemComp-HEC / 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


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7, 0.2 M sodium chloride, 20% (w/v) PEG 6000

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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 13, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.75→35.14 Å / Num. obs: 12429 / % possible obs: 93.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.076 / Rrim(I) all: 0.17 / Net I/σ(I): 9.9
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 1.171 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 490 / CC1/2: 0.4 / Rpim(I) all: 0.74 / Rrim(I) all: 1.398 / % possible all: 74.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EAD

7ead


Resolution: 1.75→35.14 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.523 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19334 614 4.9 %RANDOM
Rwork0.15839 ---
obs0.16013 11811 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å2-0.07 Å2
2---0.52 Å20 Å2
3---1.26 Å2
Refinement stepCycle: 1 / Resolution: 1.75→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 43 75 1176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131149
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151042
X-RAY DIFFRACTIONr_angle_refined_deg2.2291.7371579
X-RAY DIFFRACTIONr_angle_other_deg1.321.6212415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.30421.37351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18315164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.208155
X-RAY DIFFRACTIONr_chiral_restr0.1440.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021298
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02260
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_it1.882.294539
X-RAY DIFFRACTIONr_mcbond_other1.8722.293538
X-RAY DIFFRACTIONr_mcangle_it2.9073.436672
X-RAY DIFFRACTIONr_mcangle_other2.9063.437673
X-RAY DIFFRACTIONr_scbond_it2.7182.546610
X-RAY DIFFRACTIONr_scbond_other2.7222.55608
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3873.677907
X-RAY DIFFRACTIONr_long_range_B_refined5.41926.0891314
X-RAY DIFFRACTIONr_long_range_B_other5.36425.8971303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 39 -
Rwork0.331 709 -
obs--76.17 %

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