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- PDB-9ppo: Zn-bound structure of the H77C variant of TriCyt2 -

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Basic information

Entry
Database: PDB / ID: 9ppo
TitleZn-bound structure of the H77C variant of TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Zn-binding protein / assembly
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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)35,95310
Polymers35,6383
Non-polymers3147
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-136 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.520, 71.390, 75.840
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-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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 1500, 200 mM CaCl2, 100 mM HEPES (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.278 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 1.62→44.8 Å / Num. obs: 73610 / % possible obs: 99.85 % / Redundancy: 12.5 % / Biso Wilson estimate: 26.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04636 / Rpim(I) all: 0.01352 / Rrim(I) all: 0.04834 / Net I/σ(I): 26.98
Reflection shellResolution: 1.622→1.68 Å / Rmerge(I) obs: 0.5191 / Mean I/σ(I) obs: 12.2 / Num. unique obs: 3808 / CC1/2: 0.932 / Rpim(I) all: 0.1528 / Rrim(I) all: 0.5417

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→44.8 Å / SU ML: 0.1815 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 23.0762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2231 3801 5.16 %
Rwork0.1928 69809 -
obs0.1944 73610 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.98 Å2
Refinement stepCycle: LAST / Resolution: 1.62→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 7 216 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612561
X-RAY DIFFRACTIONf_angle_d0.73173470
X-RAY DIFFRACTIONf_chiral_restr0.0425387
X-RAY DIFFRACTIONf_plane_restr0.0061456
X-RAY DIFFRACTIONf_dihedral_angle_d13.7184967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.28621430.25282517X-RAY DIFFRACTION97.61
1.64-1.660.28271300.23222599X-RAY DIFFRACTION99.93
1.66-1.690.25431520.22392580X-RAY DIFFRACTION99.93
1.69-1.710.28491110.21982625X-RAY DIFFRACTION99.96
1.71-1.740.23841640.22532603X-RAY DIFFRACTION100
1.74-1.760.2591280.20892565X-RAY DIFFRACTION99.81
1.76-1.790.26541430.22592564X-RAY DIFFRACTION99.78
1.79-1.820.25471260.21882570X-RAY DIFFRACTION99.93
1.82-1.860.35111460.24762630X-RAY DIFFRACTION100
1.86-1.890.31831660.23382559X-RAY DIFFRACTION99.93
1.89-1.930.26711180.22622602X-RAY DIFFRACTION99.96
1.93-1.970.25591620.21662579X-RAY DIFFRACTION100
1.97-2.020.31741150.20052577X-RAY DIFFRACTION100
2.02-2.070.22241550.20942598X-RAY DIFFRACTION99.89
2.07-2.130.23351380.20172585X-RAY DIFFRACTION99.96
2.13-2.190.21571310.22615X-RAY DIFFRACTION99.96
2.19-2.260.24121540.19462567X-RAY DIFFRACTION99.96
2.26-2.340.21691410.19732593X-RAY DIFFRACTION100
2.34-2.430.27381410.19522572X-RAY DIFFRACTION99.93
2.43-2.540.23731570.2112602X-RAY DIFFRACTION99.96
2.54-2.680.24921300.20212574X-RAY DIFFRACTION99.89
2.68-2.850.21371370.20652599X-RAY DIFFRACTION100
2.85-3.070.22941360.19642598X-RAY DIFFRACTION99.96
3.07-3.370.18981420.19432588X-RAY DIFFRACTION100
3.37-3.860.23191460.16462569X-RAY DIFFRACTION99.89
3.86-4.860.16561430.16112585X-RAY DIFFRACTION100
4.87-44.80.20181460.18362594X-RAY DIFFRACTION99.93

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