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- PDB-7lsn: Ni-bound crystal structure of the engineered cyt cb562 variant, D... -

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Basic information

Entry
Database: PDB / ID: 7lsn
TitleNi-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A, crystallized in the presence of Ni(II)
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / Metal selectivity / Irving-Williams series
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
HEME C / NICKEL (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsChoi, T.S. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138884-01 United States
National Science Foundation (NSF, United States)CHE1607145 United States
CitationJournal: To Be Published
Title: Structure-guided metal selectivity in malleable protein interface mediated by single disulfide bond
Authors: Choi, T.S. / Tezcan, F.A.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Soluble cytochrome b562
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0516
Polymers23,6972
Non-polymers1,3544
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Dimeric state of protein was confirmed in mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-68 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.640, 60.660, 64.290
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: 11848.306 Da / Num. of mol.: 2 / Mutation: D60H, H63A, I67H, Q71H, T96C, T97H, A100H, K104H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG1500 25%, (NH4)2SO4 120 mM, pH 8 EPPS 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.52→30.33 Å / Num. obs: 34089 / % possible obs: 99.58 % / Redundancy: 27.7 % / Biso Wilson estimate: 19.23 Å2 / CC1/2: 0.81 / CC star: 0.946 / Rmerge(I) obs: 0.6785 / Rpim(I) all: 0.1312 / Rrim(I) all: 0.6917 / Net I/σ(I): 53.12
Reflection shellResolution: 1.52→1.574 Å / Redundancy: 28 % / Rmerge(I) obs: 1.112 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3348 / CC1/2: 0.814 / CC star: 0.947 / Rpim(I) all: 0.2145 / Rrim(I) all: 1.133 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 1.52→30.33 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 3755 5.84 %
Rwork0.2068 60506 -
obs0.2085 34033 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.93 Å2
Refinement stepCycle: LAST / Resolution: 1.52→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 2 198 1912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681759
X-RAY DIFFRACTIONf_angle_d0.80882407
X-RAY DIFFRACTIONf_chiral_restr0.0387245
X-RAY DIFFRACTIONf_plane_restr0.0054315
X-RAY DIFFRACTIONf_dihedral_angle_d11.94181231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.27731390.24992227X-RAY DIFFRACTION99.12
1.54-1.560.33821280.25282279X-RAY DIFFRACTION99.26
1.56-1.580.3181320.25522245X-RAY DIFFRACTION99.29
1.58-1.60.31251410.25212218X-RAY DIFFRACTION99.03
1.6-1.630.23581370.2372249X-RAY DIFFRACTION99.21
1.63-1.650.28451550.24292161X-RAY DIFFRACTION97.6
1.65-1.680.23841280.23652212X-RAY DIFFRACTION97.83
1.68-1.710.28181410.23882229X-RAY DIFFRACTION99.41
1.71-1.740.27391410.22672296X-RAY DIFFRACTION99.31
1.74-1.770.24611690.22142188X-RAY DIFFRACTION99.58
1.77-1.810.30851380.23312270X-RAY DIFFRACTION99.88
1.81-1.850.21551400.22862209X-RAY DIFFRACTION99.66
1.85-1.890.29721410.22722296X-RAY DIFFRACTION99.63
1.89-1.940.27851320.23392229X-RAY DIFFRACTION99.83
1.94-1.990.2161260.23132254X-RAY DIFFRACTION99.46
1.99-2.050.23391480.21892233X-RAY DIFFRACTION98.71
2.05-2.120.2361230.21342225X-RAY DIFFRACTION98.16
2.12-2.190.23561410.21222226X-RAY DIFFRACTION99.66
2.19-2.280.24631290.20982283X-RAY DIFFRACTION99.92
2.28-2.380.27231610.22032243X-RAY DIFFRACTION99.88
2.38-2.510.22881310.21022252X-RAY DIFFRACTION99.83
2.51-2.670.26411420.21482254X-RAY DIFFRACTION99.75
2.67-2.870.24021360.21192226X-RAY DIFFRACTION99.33
2.87-3.160.24231370.20772250X-RAY DIFFRACTION98.72
3.16-3.620.25461370.19452255X-RAY DIFFRACTION99.96
3.62-4.560.20251370.1772245X-RAY DIFFRACTION99.96
4.56-30.330.16351450.17042252X-RAY DIFFRACTION99.67

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