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- PDB-9pq4: Bi-bound structure of the H77C variant of TriCyt2 -

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Basic information

Entry
Database: PDB / ID: 9pq4
TitleBi-bound structure of the H77C variant of TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / 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 / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 22, 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)35,9297
Polymers35,6383
Non-polymers2904
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-49 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.840, 71.750, 76.120
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
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: 5.0.2 / Wavelength: 0.9764 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.48→45.02 Å / Num. obs: 97318 / % possible obs: 98.79 % / Redundancy: 11.8 % / Biso Wilson estimate: 16.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06106 / Rpim(I) all: 0.01791 / Rrim(I) all: 0.06371 / Net I/σ(I): 24.04
Reflection shellResolution: 1.48→1.533 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5171 / Mean I/σ(I) obs: 3.19 / Num. unique obs: 4638 / CC1/2: 0.859 / Rpim(I) all: 0.2139 / Rrim(I) all: 0.5628 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→45.02 Å / SU ML: 0.1776 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 21.4529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 3788 3.89 %
Rwork0.1574 93530 -
obs0.1598 97318 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.91 Å2
Refinement stepCycle: LAST / Resolution: 1.48→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 4 648 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332591
X-RAY DIFFRACTIONf_angle_d0.57413514
X-RAY DIFFRACTIONf_chiral_restr0.0636390
X-RAY DIFFRACTIONf_plane_restr0.004464
X-RAY DIFFRACTIONf_dihedral_angle_d12.4036979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.29391180.22963113X-RAY DIFFRACTION86.41
1.5-1.520.28771260.22183173X-RAY DIFFRACTION90.83
1.52-1.540.27431640.21283234X-RAY DIFFRACTION93.02
1.54-1.560.27521110.19763436X-RAY DIFFRACTION96.99
1.56-1.580.2221420.18523441X-RAY DIFFRACTION98.71
1.58-1.610.25751280.17773501X-RAY DIFFRACTION100
1.61-1.640.2121640.17033485X-RAY DIFFRACTION100
1.64-1.660.2091330.17963525X-RAY DIFFRACTION100
1.66-1.690.26581340.17543550X-RAY DIFFRACTION100
1.69-1.730.2451560.17223468X-RAY DIFFRACTION100
1.73-1.760.25661330.17533504X-RAY DIFFRACTION99.97
1.76-1.80.27711460.17273540X-RAY DIFFRACTION99.97
1.8-1.840.26971480.19063498X-RAY DIFFRACTION99.97
1.84-1.890.24291220.17063535X-RAY DIFFRACTION99.97
1.89-1.940.22581500.17163479X-RAY DIFFRACTION99.94
1.94-20.19731620.16253498X-RAY DIFFRACTION99.97
2-2.060.21561350.15773508X-RAY DIFFRACTION100
2.06-2.130.20431430.16123484X-RAY DIFFRACTION100
2.13-2.220.23131380.15223532X-RAY DIFFRACTION100
2.22-2.320.23311390.15773520X-RAY DIFFRACTION100
2.32-2.440.24531410.15763479X-RAY DIFFRACTION99.97
2.44-2.60.21391520.16623484X-RAY DIFFRACTION99.89
2.6-2.80.19941390.15553508X-RAY DIFFRACTION99.86
2.8-3.080.22321360.14983520X-RAY DIFFRACTION99.97
3.08-3.520.2021440.13833505X-RAY DIFFRACTION100
3.52-4.440.16721430.12363494X-RAY DIFFRACTION99.97
4.44-45.020.22351410.15843516X-RAY DIFFRACTION99.86

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