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- PDB-8rkp: Cytochrome c prime from Hydrogenophilus thermoluteolus: Ferrous r... -

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Basic information

Entry
Database: PDB / ID: 8rkp
TitleCytochrome c prime from Hydrogenophilus thermoluteolus: Ferrous recombinant native with bound NO
ComponentsCytochrome c prime
KeywordsELECTRON TRANSPORT / Nitrix oxide binding / Heme protein
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562
Similarity search - Domain/homology
ASCORBIC ACID / HEME C / NITRIC OXIDE / Cytochrome c prime
Similarity search - Component
Biological speciesHydrogenophilus thermoluteolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsFujii, S. / Hough, M.A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biophys.J. / Year: 2024
Title: Conformational rigidity of cytochrome c'-alpha from a thermophile is associated with slow NO binding.
Authors: Fujii, S. / Wilson, M.T. / Adams, H.R. / Mikolajek, H. / Svistunenko, D.A. / Smyth, P. / Andrew, C.R. / Sambongi, Y. / Hough, M.A.
History
DepositionDec 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9116
Polymers14,7341
Non-polymers1,1775
Water1,22568
1
A: Cytochrome c prime
hetero molecules

A: Cytochrome c prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,82112
Polymers29,4682
Non-polymers2,35410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area6850 Å2
ΔGint-49 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.671, 83.671, 88.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Cytochrome c prime


Mass: 14733.850 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) / Strain (production host): JCB387 / References: UniProt: F7J213
#2: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.93 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 0.2 M lithium sulphate, 30% (w/v) PEG 8,000 in a 96-well in-situ plate
Temp details: room temperature (20 C)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→72.57 Å / Num. obs: 23390 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.027 / Rrim(I) all: 0.12 / Net I/σ(I): 13.4
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 20.5 % / Rmerge(I) obs: 4.255 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1135 / CC1/2: 0.3 / Rpim(I) all: 0.952 / Rrim(I) all: 4.362 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→72.57 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.109 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21928 1131 4.8 %RANDOM
Rwork0.19727 ---
obs0.19835 22222 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.63→72.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 81 68 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161076
X-RAY DIFFRACTIONr_angle_refined_deg2.4311.7391578
X-RAY DIFFRACTIONr_angle_other_deg1.5781.6332489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73522.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.175154
X-RAY DIFFRACTIONr_chiral_restr0.3070.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021325
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02247
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_it2.8893.093545
X-RAY DIFFRACTIONr_mcbond_other2.893.084543
X-RAY DIFFRACTIONr_mcangle_it4.2114.604680
X-RAY DIFFRACTIONr_mcangle_other4.2084.614681
X-RAY DIFFRACTIONr_scbond_it5.5663.955617
X-RAY DIFFRACTIONr_scbond_other5.5653.956615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9695.666898
X-RAY DIFFRACTIONr_long_range_B_refined9.39738.3961360
X-RAY DIFFRACTIONr_long_range_B_other9.34538.2831353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 73 -
Rwork0.403 1611 -
obs--99.94 %

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