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- PDB-9wtc: Crystal structure of a selenate-soaked multiheme cytochrome c sel... -

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Basic information

Entry
Database: PDB / ID: 9wtc
TitleCrystal structure of a selenate-soaked multiheme cytochrome c selenoprotein mutant (MccSep U325A)
ComponentsCytochrome c,Multiheme cytochrome c selenoprotein (MccSep)
KeywordsELECTRON TRANSPORT / multiheme / cytochrome c / selenoprotein
Function / homologyMultiheme cytochrome superfamily / HEME C / SELENATE ION / Cytochrome c / Uncharacterized protein
Function and homology information
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMihara, H. / Yoshizawa, T. / Izu, Y. / Inoue, M. / Aono, R. / Zhang, W. / Shibamoto, N. / Tobe, R. / Kurihara, T. / Matsumura, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01994 Japan
Japan Society for the Promotion of Science (JSPS)23K18033 Japan
Japan Society for the Promotion of Science (JSPS)25H02292 Japan
CitationJournal: To Be Published
Title: Multiheme selenoenzyme essential for elemental sulfur respiration
Authors: Mihara, H. / Yoshizawa, T. / Izu, Y. / Inoue, M. / Aono, R. / Zhang, W. / Shibamoto, N. / Tobe, R. / Kurihara, T. / Matsumura, H.
History
DepositionSep 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2026Provider: 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,Multiheme cytochrome c selenoprotein (MccSep)
B: Cytochrome c,Multiheme cytochrome c selenoprotein (MccSep)
C: Cytochrome c,Multiheme cytochrome c selenoprotein (MccSep)
D: Cytochrome c,Multiheme cytochrome c selenoprotein (MccSep)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,54971
Polymers198,7624
Non-polymers15,78767
Water16,502916
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.390, 123.620, 116.640
Angle α, β, γ (deg.)90.000, 91.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome c,Multiheme cytochrome c selenoprotein (MccSep)


Mass: 49690.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Gene: GSU2937, GSU2936 / Production host: Geobacter sulfurreducens PCA (bacteria) / References: UniProt: Q748R4, UniProt: Q748R5

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Non-polymers , 5 types, 983 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SE4 / SELENATE ION


Mass: 142.958 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O4Se / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M ammonium sulfate, 0.1M HEPES (pH 7.5), 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.2→44.06 Å / Num. obs: 239402 / % possible obs: 99.91 % / Redundancy: 6.9 % / Biso Wilson estimate: 40.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07205 / Net I/σ(I): 19.89
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 23814 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.06 Å / SU ML: 0.2764 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 24.6842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 11798 5 %
Rwork0.1682 223990 -
obs0.1705 235788 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13108 0 1043 936 15087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008814765
X-RAY DIFFRACTIONf_angle_d0.978320203
X-RAY DIFFRACTIONf_chiral_restr0.05141955
X-RAY DIFFRACTIONf_plane_restr0.00762519
X-RAY DIFFRACTIONf_dihedral_angle_d16.97912063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.33723950.29747461X-RAY DIFFRACTION99.87
2.23-2.250.31953960.27997510X-RAY DIFFRACTION99.81
2.25-2.280.32043910.27717409X-RAY DIFFRACTION99.74
2.28-2.310.3183970.27527515X-RAY DIFFRACTION99.84
2.31-2.340.34763930.25817443X-RAY DIFFRACTION99.86
2.34-2.370.28633890.24467458X-RAY DIFFRACTION99.86
2.37-2.40.28373960.22867489X-RAY DIFFRACTION99.76
2.4-2.440.27453950.23457494X-RAY DIFFRACTION99.81
2.44-2.480.29123950.22127513X-RAY DIFFRACTION99.9
2.48-2.520.26533880.21537417X-RAY DIFFRACTION99.8
2.52-2.560.27243890.21597427X-RAY DIFFRACTION99.78
2.56-2.610.25094010.20487566X-RAY DIFFRACTION99.75
2.61-2.660.26023900.20097409X-RAY DIFFRACTION99.78
2.66-2.710.28583950.20197490X-RAY DIFFRACTION99.62
2.71-2.770.25863940.1997459X-RAY DIFFRACTION99.61
2.77-2.840.2773950.20627420X-RAY DIFFRACTION99.66
2.84-2.910.25063910.19837474X-RAY DIFFRACTION99.83
2.91-2.990.26553980.2017502X-RAY DIFFRACTION99.9
2.99-3.070.25533890.19257450X-RAY DIFFRACTION99.69
3.07-3.170.23683950.19227483X-RAY DIFFRACTION99.53
3.17-3.290.25773890.1827423X-RAY DIFFRACTION99.58
3.29-3.420.21843950.17077474X-RAY DIFFRACTION99.96
3.42-3.570.21673950.17397463X-RAY DIFFRACTION99.87
3.57-3.760.19253940.14957492X-RAY DIFFRACTION99.94
3.76-40.1893980.14397490X-RAY DIFFRACTION99.92
4-4.310.16893880.12787423X-RAY DIFFRACTION99.87
4.31-4.740.16013920.11467493X-RAY DIFFRACTION99.9
4.74-5.420.14173940.11697471X-RAY DIFFRACTION99.82
5.42-6.830.17623930.13497504X-RAY DIFFRACTION99.76
6.83-44.060.14973880.13047368X-RAY DIFFRACTION98.6

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