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- PDB-9ppt: Ni- and Bi-bound structure of the H77C variant of TriCyt2 -

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Basic information

Entry
Database: PDB / ID: 9ppt
TitleNi- and Bi-bound structure of the H77C variant of TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Ni- and Bi-binding protein / assembly
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Bismuth(III) ION / NICKEL (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsEng, V.H. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
National Science Foundation (NSF, United States)DGE-2038238 United States
CitationJournal: J.Inorg.Biochem. / Year: 2025
Title: Design of a protein scaffold with a selective, Bi-containing heterodinuclear metal coordination motif.
Authors: Eng, V.H. / Gascon, M. / Kakkis, A. / Tezcan, F.A.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9466
Polymers35,6383
Non-polymers3083
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-52 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.150, 70.540, 75.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11879.474 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: cybC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABE7
#2: Chemical ChemComp-BS3 / Bismuth(III) ION


Mass: 208.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Bi / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 1500, 200 mM CaCl2, 100 mM MES (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.476 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.476 Å / Relative weight: 1
ReflectionResolution: 1.78→45.1 Å / Num. obs: 55302 / % possible obs: 99.94 % / Redundancy: 12.1 % / Biso Wilson estimate: 29.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06377 / Rpim(I) all: 0.01884 / Rrim(I) all: 0.06656 / Net I/σ(I): 23.69
Reflection shellResolution: 1.784→1.847 Å / Rmerge(I) obs: 0.8935 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 2883 / CC1/2: 0.565 / Rpim(I) all: 0.3053 / Rrim(I) all: 0.946

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→45.1 Å / SU ML: 0.2872 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 28.5204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2665 3744 6.77 %
Rwork0.2123 51558 -
obs0.216 55302 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.73 Å2
Refinement stepCycle: LAST / Resolution: 1.78→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 3 369 2871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182595
X-RAY DIFFRACTIONf_angle_d0.39483521
X-RAY DIFFRACTIONf_chiral_restr0.0333390
X-RAY DIFFRACTIONf_plane_restr0.0035465
X-RAY DIFFRACTIONf_dihedral_angle_d10.9674980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.37871330.34321906X-RAY DIFFRACTION98.88
1.81-1.830.37321380.33151857X-RAY DIFFRACTION100
1.83-1.860.32181590.30181920X-RAY DIFFRACTION100
1.86-1.880.32131320.28581947X-RAY DIFFRACTION99.95
1.88-1.910.32721440.29371857X-RAY DIFFRACTION100
1.91-1.940.3251290.29691935X-RAY DIFFRACTION100
1.94-1.970.29731290.28261920X-RAY DIFFRACTION100
1.97-2.010.34651480.2731925X-RAY DIFFRACTION100
2.01-2.040.26631400.26521896X-RAY DIFFRACTION99.95
2.04-2.080.29521300.25361917X-RAY DIFFRACTION100
2.08-2.120.31330.2551910X-RAY DIFFRACTION100
2.12-2.170.30351390.25361921X-RAY DIFFRACTION100
2.17-2.220.29561510.23651898X-RAY DIFFRACTION99.95
2.22-2.280.29081420.23451889X-RAY DIFFRACTION99.9
2.28-2.340.29681480.24211922X-RAY DIFFRACTION100
2.34-2.410.28491340.25471898X-RAY DIFFRACTION100
2.41-2.480.31441210.25631929X-RAY DIFFRACTION100
2.48-2.570.25431560.23691910X-RAY DIFFRACTION100
2.57-2.680.38451390.25261915X-RAY DIFFRACTION100
2.68-2.80.27861290.24291921X-RAY DIFFRACTION100
2.8-2.940.29371240.21931936X-RAY DIFFRACTION99.95
2.94-3.130.32681500.21831883X-RAY DIFFRACTION100
3.13-3.370.27551430.18951910X-RAY DIFFRACTION100
3.37-3.710.2021440.16911904X-RAY DIFFRACTION100
3.71-4.250.20731350.15291911X-RAY DIFFRACTION100
4.25-5.350.20481490.15841898X-RAY DIFFRACTION100
5.35-45.10.24081250.18091923X-RAY DIFFRACTION99.95

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