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- PDB-9ppm: Mn-bound structure of the H77C variant of TriCyt2 -

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Basic information

Entry
Database: PDB / ID: 9ppm
TitleMn-bound structure of the H77C variant of TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Manganese-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
: / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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
D: Soluble cytochrome b562
E: Soluble cytochrome b562
F: Soluble cytochrome b562
G: Soluble cytochrome b562
H: Soluble cytochrome b562
I: Soluble cytochrome b562
J: Soluble cytochrome b562
K: Soluble cytochrome b562
L: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,79617
Polymers142,55412
Non-polymers2435
Water61334
1
A: Soluble cytochrome b562
C: Soluble cytochrome b562
H: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7165
Polymers35,6383
Non-polymers782
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-32 kcal/mol
Surface area15110 Å2
MethodPISA
2
B: Soluble cytochrome b562
E: Soluble cytochrome b562
G: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6934
Polymers35,6383
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-23 kcal/mol
Surface area15250 Å2
MethodPISA
3
F: Soluble cytochrome b562
K: Soluble cytochrome b562
hetero molecules

D: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)35,6934
Polymers35,6383
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3310 Å2
ΔGint-20 kcal/mol
Surface area15200 Å2
MethodPISA
4
J: Soluble cytochrome b562
L: Soluble cytochrome b562
hetero molecules

I: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)35,6934
Polymers35,6383
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3280 Å2
ΔGint-21 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.190, 47.360, 166.230
Angle α, β, γ (deg.)90.000, 97.270, 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

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


Mass: 11879.474 Da / Num. of mol.: 12
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.95 Å3/Da / Density % sol: 36.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 1500, 200 mM NH4OAc, 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: 8.3.1 / Wavelength: 1.878 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.878 Å / Relative weight: 1
ReflectionResolution: 2.53→46.31 Å / Num. obs: 71610 / % possible obs: 99.65 % / Redundancy: 6.4 % / Biso Wilson estimate: 57.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06042 / Rpim(I) all: 0.02597 / Rrim(I) all: 0.06591 / Net I/σ(I): 17.43
Reflection shellResolution: 2.53→2.62 Å / Rmerge(I) obs: 0.4934 / Num. unique obs: 3671 / CC1/2: 0.876 / Rpim(I) all: 0.2167 / Rrim(I) all: 0.5406

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→46.31 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 33.3419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2915 3825 5.34 %
Rwork0.2335 67785 -
obs0.2366 71610 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.81 Å2
Refinement stepCycle: LAST / Resolution: 2.53→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9996 0 5 34 10035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003210178
X-RAY DIFFRACTIONf_angle_d0.566213774
X-RAY DIFFRACTIONf_chiral_restr0.03221538
X-RAY DIFFRACTIONf_plane_restr0.00421804
X-RAY DIFFRACTIONf_dihedral_angle_d4.42551324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.560.38471300.3332279X-RAY DIFFRACTION91.39
2.56-2.590.38781460.32332586X-RAY DIFFRACTION99.78
2.59-2.630.35531390.32072570X-RAY DIFFRACTION99.52
2.63-2.670.41381380.31682473X-RAY DIFFRACTION99.73
2.67-2.710.4131390.342453X-RAY DIFFRACTION99.88
2.71-2.750.41631520.33392585X-RAY DIFFRACTION99.93
2.75-2.790.35711440.31182509X-RAY DIFFRACTION99.7
2.79-2.840.36091390.29782530X-RAY DIFFRACTION99.7
2.84-2.890.3651410.29732468X-RAY DIFFRACTION99.5
2.89-2.950.37121460.28642618X-RAY DIFFRACTION100
2.95-3.010.38811380.27632427X-RAY DIFFRACTION99.77
3.01-3.070.27731460.29022573X-RAY DIFFRACTION99.89
3.07-3.150.38311470.2912535X-RAY DIFFRACTION99.44
3.15-3.220.36951440.29652461X-RAY DIFFRACTION99.62
3.22-3.310.33551440.28752557X-RAY DIFFRACTION99.89
3.31-3.410.32991430.27012550X-RAY DIFFRACTION99.63
3.41-3.520.33061370.24912462X-RAY DIFFRACTION99.69
3.52-3.640.331390.23232579X-RAY DIFFRACTION99.31
3.64-3.790.32341360.21762434X-RAY DIFFRACTION99.19
3.79-3.960.32251440.21172608X-RAY DIFFRACTION99.24
3.96-4.170.25681430.20432458X-RAY DIFFRACTION99.96
4.17-4.430.23891410.19692534X-RAY DIFFRACTION99.55
4.43-4.770.26981460.18442553X-RAY DIFFRACTION99.85
4.77-5.250.26681400.20152485X-RAY DIFFRACTION98.68
5.25-6.010.25751430.2432507X-RAY DIFFRACTION99.55
6.02-7.570.20751370.21212504X-RAY DIFFRACTION99.36
7.57-46.310.17521430.15692487X-RAY DIFFRACTION97.95

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