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- PDB-7lr5: Ni-bound crystal structure of the engineered cyt cb562 variant, D... -

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Basic information

Entry
Database: PDB / ID: 7lr5
TitleNi-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Ni(II) (M1) and Cu(II) (M2)
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: 1.7 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: Nature / Year: 2022
Title: Overcoming universal restrictions on metal selectivity by protein design.
Authors: Choi, T.S. / Tezcan, F.A.
History
DepositionFeb 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,1856
Polymers23,8312
Non-polymers1,3544
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Dimeric state and shape of protein were confirmed in solution SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-66 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 60.920, 63.160
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: 11915.375 Da / Num. of mol.: 2 / Mutation: D60H, I67H, Q71H, 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.: 174 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG1500 25%, pH 8 EPPS 100 mM, No salt,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.7→41.32 Å / Num. obs: 23765 / % possible obs: 99.5 % / Redundancy: 38.7 % / Biso Wilson estimate: 17.96 Å2 / CC1/2: 0.878 / CC star: 0.967 / Rmerge(I) obs: 0.7238 / Rpim(I) all: 0.1161 / Rrim(I) all: 0.7335 / Net I/σ(I): 35.1
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 36.7 % / Rmerge(I) obs: 0.9307 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 2334 / CC1/2: 0.727 / CC star: 0.918 / Rpim(I) all: 0.156 / Rrim(I) all: 0.9442 / % possible all: 99.62

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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: 1.7→41.32 Å / SU ML: 0.1948 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.4261
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 3749 8.47 %
Rwork0.1893 40537 -
obs0.1926 23704 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.56 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 2 174 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681769
X-RAY DIFFRACTIONf_angle_d0.80222420
X-RAY DIFFRACTIONf_chiral_restr0.0393245
X-RAY DIFFRACTIONf_plane_restr0.0049316
X-RAY DIFFRACTIONf_dihedral_angle_d11.80061235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.30081310.23351471X-RAY DIFFRACTION96.8
1.72-1.740.27981570.20821477X-RAY DIFFRACTION98.91
1.74-1.770.24681320.20191520X-RAY DIFFRACTION99.34
1.77-1.790.2721610.20481492X-RAY DIFFRACTION98.86
1.79-1.820.24631270.2031520X-RAY DIFFRACTION98.98
1.82-1.850.24241180.20751492X-RAY DIFFRACTION98.59
1.85-1.880.23471600.19691469X-RAY DIFFRACTION96.91
1.88-1.910.24131270.19971515X-RAY DIFFRACTION98.09
1.91-1.950.27241560.19821485X-RAY DIFFRACTION99.09
1.95-1.980.2341030.18791519X-RAY DIFFRACTION99.14
1.98-2.020.24091530.19291508X-RAY DIFFRACTION99.64
2.02-2.070.22081320.19451491X-RAY DIFFRACTION98.84
2.07-2.120.24561390.18711524X-RAY DIFFRACTION98.58
2.12-2.170.24271330.19711443X-RAY DIFFRACTION97.1
2.17-2.230.22521510.1931493X-RAY DIFFRACTION98.86
2.23-2.290.26761390.19441539X-RAY DIFFRACTION99.76
2.29-2.370.29121290.18931509X-RAY DIFFRACTION99.45
2.37-2.450.22541340.20451530X-RAY DIFFRACTION99.58
2.45-2.550.26791480.19051518X-RAY DIFFRACTION99.88
2.55-2.670.24621350.19251459X-RAY DIFFRACTION98.15
2.67-2.810.22581240.20861531X-RAY DIFFRACTION99.04
2.81-2.980.2271410.20231520X-RAY DIFFRACTION99.94
2.98-3.210.28991410.20411510X-RAY DIFFRACTION99.04
3.21-3.540.22181400.19031499X-RAY DIFFRACTION99.15
3.54-4.050.21541510.17251477X-RAY DIFFRACTION98.31
4.05-5.10.16581410.16151521X-RAY DIFFRACTION99.82
5.1-41.320.15881460.1561505X-RAY DIFFRACTION99.58

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