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- PDB-7yr9: Crystal structure of the immature form of TtPetA -

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Basic information

Entry
Database: PDB / ID: 7yr9
TitleCrystal structure of the immature form of TtPetA
ComponentsUbiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsELECTRON TRANSPORT / Rieske / iron-sulfur cluster / metal binding
Function / homology
Function and homology information


quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / 2 iron, 2 sulfur cluster binding / metal ion binding / plasma membrane
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Ubiquinol-cytochrome c reductase iron-sulfur subunit
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsTsutsumi, E. / Niwa, S. / Takeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: Commun Chem / Year: 2023
Title: Structure of a putative immature form of a Rieske-type iron-sulfur protein in complex with zinc chloride.
Authors: Tsutsumi, E. / Niwa, S. / Takeda, R. / Sakamoto, N. / Okatsu, K. / Fukai, S. / Ago, H. / Nagao, S. / Sekiguchi, H. / Takeda, K.
History
DepositionAug 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: Ubiquinol-cytochrome c reductase iron-sulfur subunit
B: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,93316
Polymers32,9002
Non-polymers1,03314
Water2,612145
1
A: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules

B: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,93316
Polymers32,9002
Non-polymers1,03314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Unit cell
Length a, b, c (Å)32.596, 98.711, 51.052
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit / TtPetA


Mass: 16449.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochromatium tepidum (bacteria) / Gene: petA / Production host: Escherichia coli (E. coli) / References: UniProt: D1MZ11, quinol-cytochrome-c reductase

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Non-polymers , 5 types, 159 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M AmS, 20% glycerol, 0.1 M Na-Ac pH 4.6

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Data collection

DiffractionMean temperature: 15 K / Ambient temp details: He cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2825 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.256
ReflectionResolution: 1.7→50 Å / Num. obs: 34104 / % possible obs: 95.7 % / Redundancy: 7.09 % / Biso Wilson estimate: 21.741 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.084 / Χ2: 0.9 / Net I/σ(I): 15.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.87.0040.3034.7237318576153280.9640.32792.5
1.8-1.927.2150.216.9336586538850710.9850.22694.1
1.92-2.087.3050.15110.2734954503347850.9910.16295.1
2.08-2.286.9290.11313.7730607460844170.9930.12295.9
2.28-2.547.0170.09117.328383419640450.9960.09896.4
2.54-2.947.3860.0821.4626559369835960.9960.08697.2
2.94-3.597.1050.05729.4222018316230990.9980.06298
3.59-5.066.7140.04635.6816127243124020.9990.04998.8
5.06-506.9110.04736.139406137413610.9990.0599.1

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 33923
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7-10044.80.75505
5.54-741.40.797508
4.75-5.5433.20.818608
4.22-4.7533.50.843698
3.84-4.2234.50.827757
3.54-3.8439.20.805822
3.31-3.5437.90.807895
3.11-3.3137.50.799963
2.95-3.11380.796975
2.81-2.9538.20.7641045
2.69-2.8140.50.7611075
2.58-2.6943.20.751159
2.48-2.5837.80.7631171
2.4-2.4840.60.7411251
2.32-2.440.60.7521206
2.25-2.3239.70.741316
2.19-2.2540.50.7271315
2.13-2.1940.90.7241393
2.07-2.1342.20.7191380
2.02-2.0744.90.7021412
1.98-2.0247.90.6771479
1.93-1.9847.80.681494
1.89-1.9348.50.6411498
1.85-1.89520.6081569
1.82-1.8553.20.591535
1.78-1.8257.30.5431626
1.75-1.7859.60.5271654
1.7-1.7562.60.4952614

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SOLVE2.13phasing
DM7.0.078phasing
CNSrefinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 2885
RfactorNum. reflection% reflection
Rfree0.2341 1655 4.5 %
Rwork0.2037 61062 -
obs-34104 91.7 %
Solvent computationBsol: 57.4944 Å2
Displacement parametersBiso max: 75 Å2 / Biso mean: 15.9042 Å2 / Biso min: 4.65 Å2
Baniso -1Baniso -2Baniso -3
1--3.693 Å20 Å21.893 Å2
2--6.066 Å20 Å2
3----2.374 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 48 145 2465
Biso mean--46.09 19.1 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.9481.5
X-RAY DIFFRACTIONc_scbond_it1.7022
X-RAY DIFFRACTIONc_mcangle_it1.4312
X-RAY DIFFRACTIONc_scangle_it2.4552.5
LS refinement shellResolution: 1.7→1.78 Å
RfactorNum. reflection
Rfree0.2962 -
Rwork0.2705 -
obs-7529
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6so4.param
X-RAY DIFFRACTION7gol.param

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