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- PDB-9ppn: Cu-bound structure of the H77C variant of TriCyt2 -

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Basic information

Entry
Database: PDB / ID: 9ppn
TitleCu-bound structure of the H77C variant of TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Cu-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
COPPER (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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)35,7024
Polymers35,6383
Non-polymers641
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-37 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.630, 71.080, 75.600
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 41.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 21% 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: 1.369 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: 1.369 Å / Relative weight: 1
ReflectionResolution: 1.87→44.81 Å / Num. obs: 48138 / % possible obs: 99.97 % / Redundancy: 13.2 % / Biso Wilson estimate: 30.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08648 / Rpim(I) all: 0.02479 / Rrim(I) all: 0.09003 / Net I/σ(I): 20.83
Reflection shellResolution: 1.87→1.937 Å / Mean I/σ(I) obs: 2.33 / Num. unique obs: 2473 / CC1/2: 0.826 / Rpim(I) all: 0.32

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→44.81 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 23.438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 3751 7.79 %
Rwork0.1811 44387 -
obs0.1842 48138 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.11 Å2
Refinement stepCycle: LAST / Resolution: 1.87→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 1 282 2782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562564
X-RAY DIFFRACTIONf_angle_d0.67823474
X-RAY DIFFRACTIONf_chiral_restr0.0421387
X-RAY DIFFRACTIONf_plane_restr0.0053457
X-RAY DIFFRACTIONf_dihedral_angle_d13.4363967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.890.34031320.29541636X-RAY DIFFRACTION98.72
1.89-1.910.34781480.27031668X-RAY DIFFRACTION99.89
1.91-1.940.2761340.24631591X-RAY DIFFRACTION100
1.94-1.970.25241510.23391650X-RAY DIFFRACTION99.94
1.97-20.28051430.22851671X-RAY DIFFRACTION99.94
2-2.030.2761480.2111625X-RAY DIFFRACTION100
2.03-2.060.32281280.21331662X-RAY DIFFRACTION100
2.06-2.10.20441340.19441643X-RAY DIFFRACTION100
2.1-2.140.23261300.20141661X-RAY DIFFRACTION100
2.14-2.180.25791430.18721606X-RAY DIFFRACTION100
2.18-2.220.24291410.18481651X-RAY DIFFRACTION100
2.22-2.270.26621470.18311644X-RAY DIFFRACTION100
2.27-2.320.28681170.19671644X-RAY DIFFRACTION100
2.32-2.380.22971510.18351651X-RAY DIFFRACTION100
2.38-2.450.21881480.19541649X-RAY DIFFRACTION100
2.45-2.520.30651280.19311657X-RAY DIFFRACTION100
2.52-2.60.22451390.1981633X-RAY DIFFRACTION100
2.6-2.690.28981420.20161633X-RAY DIFFRACTION100
2.69-2.80.26781360.2021675X-RAY DIFFRACTION100
2.8-2.930.25051390.1991652X-RAY DIFFRACTION99.94
2.93-3.080.26371510.19181605X-RAY DIFFRACTION100
3.08-3.270.18591400.19721655X-RAY DIFFRACTION100
3.27-3.530.22651260.16271638X-RAY DIFFRACTION100
3.53-3.880.1761360.15171642X-RAY DIFFRACTION100
3.88-4.440.17381290.14041667X-RAY DIFFRACTION100
4.44-5.60.18061470.15771648X-RAY DIFFRACTION100
5.6-44.810.16511430.17041630X-RAY DIFFRACTION99.89

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