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- PDB-9pnh: Ni-bound structure of the H77C variant of TriCyt2 -

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Basic information

Entry
Database: PDB / ID: 9pnh
TitleNi-bound structure of the H77C variant of TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Nickel-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
NICKEL (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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

Downloads & links

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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)35,7736
Polymers35,6383
Non-polymers1343
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-52 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.960, 71.320, 75.660
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-NI / NICKEL (II) ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 217 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
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: 1.477 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: 1.477 Å / Relative weight: 1
ReflectionResolution: 1.84→44.99 Å / Num. obs: 50440 / % possible obs: 99.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 34.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0595 / Rpim(I) all: 0.01771 / Rrim(I) all: 0.06217 / Net I/σ(I): 24.1
Reflection shellResolution: 1.842→1.908 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.0595 / Mean I/σ(I) obs: 3.26 / Num. unique obs: 2583 / CC1/2: 0.926 / Rpim(I) all: 0.01771 / Rrim(I) all: 0.06217 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→44.99 Å / SU ML: 0.2484 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 24.0759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 3784 7.5 %
Rwork0.1888 46656 -
obs0.1918 50440 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.25 Å2
Refinement stepCycle: LAST / Resolution: 1.84→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 4 217 2720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852560
X-RAY DIFFRACTIONf_angle_d0.86863467
X-RAY DIFFRACTIONf_chiral_restr0.0462386
X-RAY DIFFRACTIONf_plane_restr0.0072455
X-RAY DIFFRACTIONf_dihedral_angle_d13.7133964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.870.44371320.34691643X-RAY DIFFRACTION95.33
1.87-1.890.31871330.30561738X-RAY DIFFRACTION100
1.89-1.920.2871400.26271737X-RAY DIFFRACTION100
1.92-1.940.33341390.23561730X-RAY DIFFRACTION100
1.94-1.970.27051230.22721747X-RAY DIFFRACTION99.95
1.97-20.24291830.21441699X-RAY DIFFRACTION100
2-2.040.29531180.20451778X-RAY DIFFRACTION99.95
2.04-2.070.21441360.2021732X-RAY DIFFRACTION99.84
2.07-2.110.26641550.19651715X-RAY DIFFRACTION99.95
2.11-2.150.24791390.19811721X-RAY DIFFRACTION100
2.15-2.190.24721300.19581720X-RAY DIFFRACTION100
2.19-2.240.24211550.18891745X-RAY DIFFRACTION99.95
2.24-2.290.27311430.20391705X-RAY DIFFRACTION99.89
2.29-2.350.26561240.20291756X-RAY DIFFRACTION100
2.35-2.410.21541310.19631749X-RAY DIFFRACTION99.79
2.41-2.480.31471450.20161712X-RAY DIFFRACTION99.95
2.49-2.560.2711450.20411740X-RAY DIFFRACTION99.89
2.57-2.660.29231430.20141738X-RAY DIFFRACTION100
2.66-2.760.25081490.21491712X-RAY DIFFRACTION99.95
2.76-2.890.27841270.20221748X-RAY DIFFRACTION99.89
2.89-3.040.27321420.19771731X-RAY DIFFRACTION99.79
3.04-3.230.21360.20951733X-RAY DIFFRACTION100
3.23-3.480.23041510.17691725X-RAY DIFFRACTION100
3.48-3.830.20731370.1641720X-RAY DIFFRACTION99.84
3.83-4.390.16441480.14621720X-RAY DIFFRACTION99.68
4.39-5.520.20461400.1631734X-RAY DIFFRACTION100
5.53-44.990.18261400.19041728X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.653798737310.2430668468160.2490266460676.872206242171.594737369344.14462561568-0.1430449187590.519750862205-0.586037733762-0.3467496246110.0324602150479-0.03226069200430.315027099233-0.118044466860.1569190746810.255965030621-0.09349814129120.0268460114440.258301009087-0.06143473373120.2819484846935.293784217537.3073155646913.9938420457
24.18887669182-0.550808327255-0.5718569341357.554623260732.669986735377.73719437977-0.125164873602-0.102186210696-0.2821198050290.180880882736-0.03657321083570.0808696493544-0.0368770234025-0.03356829932650.1267901240320.163301312149-0.0372137064193-0.04535683974060.1838657583320.062930030030.21786108247311.079068793215.262774029521.3803762885
38.72674525983-1.31843956645-5.146821121313.911214535691.936246080957.52394744473-0.04698053965750.0946699196123-0.82174943052-0.0145890990915-0.230152264734-0.5015409424020.3486591928710.5779002879510.2275293568620.3773416512430.00835347926872-0.01303828144380.3132361849250.03873040826450.45641177843611.49004163163.0489951083320.4811249096
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 48 )1 - 481 - 48
22chain 'A' and (resid 49 through 80 )49 - 8049 - 80
33chain 'A' and (resid 81 through 106 )81 - 10681 - 106

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