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

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Basic information

Entry
Database: PDB / ID: 7lrv
TitleNi-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, 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: 1.4 Å
AuthorsChoi, T.S. / Tezcan, F.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1607145 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138884-01 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 17, 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

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)25,1856
Polymers23,8312
Non-polymers1,3544
Water4,522251
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 area3380 Å2
ΔGint-69 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 60.720, 63.770
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, 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.: 251 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG1500 25%, pH 8 EPPS 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.4→41.61 Å / Num. obs: 42610 / % possible obs: 99.8 % / Redundancy: 32.2 % / Biso Wilson estimate: 16.52 Å2 / CC1/2: 0.738 / Rmerge(I) obs: 0.744 / Rpim(I) all: 0.1333 / Rrim(I) all: 0.7563 / Net I/σ(I): 152.76
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 28.3 % / Rmerge(I) obs: 0.9591 / Mean I/σ(I) obs: 9.62 / Num. unique obs: 4185 / CC1/2: 0.804 / CC star: 0.944 / Rpim(I) all: 0.1631 / Rrim(I) all: 0.9731 / % possible all: 99.12

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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: 1.4→41.61 Å / SU ML: 0.1242 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 3764 4.65 %
Rwork0.1901 77175 -
obs0.1913 42605 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 2 251 1967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591770
X-RAY DIFFRACTIONf_angle_d0.78092426
X-RAY DIFFRACTIONf_chiral_restr0.0603246
X-RAY DIFFRACTIONf_plane_restr0.0052318
X-RAY DIFFRACTIONf_dihedral_angle_d12.92981018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.23411410.21072851X-RAY DIFFRACTION98.65
1.42-1.440.24591380.20412809X-RAY DIFFRACTION99.29
1.44-1.460.2921370.21282849X-RAY DIFFRACTION98.87
1.46-1.480.24031700.20712837X-RAY DIFFRACTION99.24
1.48-1.50.22091080.20132863X-RAY DIFFRACTION99.36
1.5-1.520.20081250.19632847X-RAY DIFFRACTION99.07
1.52-1.550.22781470.1822862X-RAY DIFFRACTION100
1.55-1.570.2281420.19342840X-RAY DIFFRACTION99.53
1.57-1.60.23461570.18932811X-RAY DIFFRACTION99.7
1.6-1.630.23811300.18952887X-RAY DIFFRACTION99.93
1.63-1.670.21561460.19662850X-RAY DIFFRACTION99.83
1.67-1.70.18891250.19462882X-RAY DIFFRACTION99.87
1.7-1.740.23621540.19982843X-RAY DIFFRACTION99.97
1.74-1.790.21211390.20042904X-RAY DIFFRACTION99.93
1.79-1.830.24851310.20652852X-RAY DIFFRACTION100
1.83-1.890.25441510.19792846X-RAY DIFFRACTION100
1.89-1.950.20951340.20342886X-RAY DIFFRACTION100
1.95-2.020.26021400.20232844X-RAY DIFFRACTION100
2.02-2.10.21411410.19762890X-RAY DIFFRACTION100
2.1-2.20.2111400.19852871X-RAY DIFFRACTION100
2.2-2.310.24211420.19362860X-RAY DIFFRACTION100
2.31-2.460.24331420.1982840X-RAY DIFFRACTION100
2.46-2.650.22251410.18962874X-RAY DIFFRACTION100
2.65-2.910.24021330.1942880X-RAY DIFFRACTION100
2.91-3.330.25581440.19642850X-RAY DIFFRACTION100
3.33-4.20.17411340.17532876X-RAY DIFFRACTION100
4.2-41.610.15791320.16782871X-RAY DIFFRACTION99.97

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