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

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Basic information

Entry
Database: PDB / ID: 7lrb
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 / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
Revision 2.0Apr 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_rmsd_bond / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id
Revision 2.1Nov 6, 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
A: Soluble cytochrome b562
B: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1866
Polymers23,8312
Non-polymers1,3554
Water3,963220
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 area3490 Å2
ΔGint-68 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 61.050, 64.300
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG1500 25%, Ammonium acetate 160 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: 1.59 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2020
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.59 Å / Relative weight: 1
ReflectionResolution: 1.78→41.63 Å / Num. obs: 20861 / % possible obs: 97.65 % / Redundancy: 26 % / Biso Wilson estimate: 17.17 Å2 / CC1/2: 0.676 / CC star: 0.898 / Rmerge(I) obs: 0.7359 / Rpim(I) all: 0.1447 / Rrim(I) all: 0.7509 / Net I/σ(I): 31.17
Reflection shellResolution: 1.78→1.844 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.7766 / Mean I/σ(I) obs: 6.16 / Num. unique obs: 1911 / CC1/2: 0.788 / CC star: 0.939 / Rpim(I) all: 0.1692 / Rrim(I) all: 0.7961 / % possible all: 91.7

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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: 1.78→41.63 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2315
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 3665 9.54 %
Rwork0.1774 34751 -
obs0.1807 20721 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.86 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 4 220 1947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061820
X-RAY DIFFRACTIONf_angle_d0.86382500
X-RAY DIFFRACTIONf_chiral_restr0.0427252
X-RAY DIFFRACTIONf_plane_restr0.0049329
X-RAY DIFFRACTIONf_dihedral_angle_d11.21471470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.29651310.23521133X-RAY DIFFRACTION83.1
1.8-1.830.2361240.21651269X-RAY DIFFRACTION90.69
1.83-1.850.31741260.20851359X-RAY DIFFRACTION97.5
1.85-1.880.2581690.18681326X-RAY DIFFRACTION97.46
1.88-1.910.21191430.18031345X-RAY DIFFRACTION96.94
1.91-1.940.21871190.16831366X-RAY DIFFRACTION96.81
1.94-1.980.22421340.18661329X-RAY DIFFRACTION96.25
1.98-2.010.26971440.1851309X-RAY DIFFRACTION93.44
2.01-2.050.20371530.19911344X-RAY DIFFRACTION97.97
2.05-2.090.2671310.17631367X-RAY DIFFRACTION98.04
2.09-2.140.21781370.17421337X-RAY DIFFRACTION97.62
2.14-2.190.20741480.17251356X-RAY DIFFRACTION97.6
2.19-2.240.20171470.18651320X-RAY DIFFRACTION96.32
2.24-2.30.27511240.1821329X-RAY DIFFRACTION94.05
2.3-2.370.24591550.18111359X-RAY DIFFRACTION98.31
2.37-2.450.26531400.18431332X-RAY DIFFRACTION98.07
2.45-2.540.21411370.17331386X-RAY DIFFRACTION98.26
2.54-2.640.21231650.19051334X-RAY DIFFRACTION97.59
2.64-2.760.20711420.18341340X-RAY DIFFRACTION97.12
2.76-2.90.22161380.1831344X-RAY DIFFRACTION96.17
2.9-3.080.22991480.19111345X-RAY DIFFRACTION98.94
3.08-3.320.18491470.18731382X-RAY DIFFRACTION99.67
3.32-3.660.19761370.16771366X-RAY DIFFRACTION97.79
3.66-4.180.20071470.16021336X-RAY DIFFRACTION96.17
4.18-5.270.15911260.15151389X-RAY DIFFRACTION99.61
5.27-41.630.15181530.1591349X-RAY DIFFRACTION97.72

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