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

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Basic information

Entry
Database: PDB / ID: 7lra
TitleNi-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in the presence of Cu(II) (M1) and Ni(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 16, 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

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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
Water4,414245
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 area3300 Å2
ΔGint-66 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 61.000, 64.160
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.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: PEG1500 25%, Ammonium acetate 200 mM, pH 8.4 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: 1.48 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.7→41.65 Å / Num. obs: 24213 / % possible obs: 99.54 % / Redundancy: 28.4 % / Biso Wilson estimate: 17.98 Å2 / CC1/2: 0.73 / CC star: 0.919 / Rmerge(I) obs: 0.7754 / Rpim(I) all: 0.1475 / Rrim(I) all: 0.79 / Net I/σ(I): 49.46
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 26.8 % / Rmerge(I) obs: 0.8503 / Mean I/σ(I) obs: 8.63 / Num. unique obs: 2371 / CC1/2: 0.771 / CC star: 0.933 / Rpim(I) all: 0.1641 / Rrim(I) all: 0.8665 / % possible all: 99.37

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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→41.65 Å / SU ML: 0.1718 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 3769 8.34 %
Rwork0.1802 41441 -
obs0.1831 24165 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 2 245 1963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641768
X-RAY DIFFRACTIONf_angle_d0.77512420
X-RAY DIFFRACTIONf_chiral_restr0.0402244
X-RAY DIFFRACTIONf_plane_restr0.0054317
X-RAY DIFFRACTIONf_dihedral_angle_d11.67161244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.28381300.22831498X-RAY DIFFRACTION96.9
1.72-1.740.2351420.22571543X-RAY DIFFRACTION99
1.74-1.770.22631310.18931549X-RAY DIFFRACTION99.12
1.77-1.790.22061520.18671533X-RAY DIFFRACTION99.18
1.79-1.820.22091150.17641547X-RAY DIFFRACTION99.11
1.82-1.850.18611400.18081517X-RAY DIFFRACTION98.4
1.85-1.880.19821460.18311495X-RAY DIFFRACTION97.1
1.88-1.910.26251310.18561516X-RAY DIFFRACTION97.69
1.91-1.950.24551360.19771540X-RAY DIFFRACTION99.17
1.95-1.980.27091500.18921524X-RAY DIFFRACTION99.76
1.98-2.020.19481500.18921572X-RAY DIFFRACTION99.65
2.02-2.070.28641280.17811521X-RAY DIFFRACTION99.16
2.07-2.120.20951630.17451533X-RAY DIFFRACTION99.12
2.12-2.170.19841430.18241517X-RAY DIFFRACTION97.42
2.17-2.230.20371210.18451524X-RAY DIFFRACTION98.56
2.23-2.290.26791410.18321538X-RAY DIFFRACTION99.82
2.29-2.370.21341500.18871572X-RAY DIFFRACTION99.83
2.37-2.450.1981250.19281532X-RAY DIFFRACTION99.46
2.45-2.550.25651400.18111555X-RAY DIFFRACTION99.41
2.55-2.670.27291330.18771521X-RAY DIFFRACTION97.87
2.67-2.810.21281440.19071532X-RAY DIFFRACTION99
2.81-2.980.18611420.19241546X-RAY DIFFRACTION99.94
2.98-3.210.24511520.19931538X-RAY DIFFRACTION99.82
3.21-3.540.21021300.17231557X-RAY DIFFRACTION99.88
3.54-4.050.20351360.16331545X-RAY DIFFRACTION99.17
4.05-5.10.17461380.15981549X-RAY DIFFRACTION100
5.1-41.650.16831600.15641527X-RAY DIFFRACTION99.59

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