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- PDB-7mk4: Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 -

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Basic information

Entry
Database: PDB / ID: 7mk4
TitleCo-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
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 / MOLECULAR REPLACEMENT / Resolution: 1.27 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
DepositionApr 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: 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 18, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _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 2.1Oct 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

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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
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Solution SAXS data of the protein is included in the paper.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-70 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.529, 61.075, 64.572
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
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.: 362 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: PEG1500 25%, NaCl 140 mM, pH 6.6 MES 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.269→34.42 Å / Num. obs: 57551 / % possible obs: 99.79 % / Redundancy: 7.2 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Rrim(I) all: 0.072 / Net I/σ(I): 10
Reflection shellResolution: 1.269→1.315 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5614 / CC1/2: 0.765 / Rpim(I) all: 0.429 / Rrim(I) all: 0.953 / % possible all: 98.86

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Processing

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

2bc5


Resolution: 1.27→34.42 Å / SU ML: 0.1663 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 3813 3.47 %
Rwork0.196 105933 -
obs0.1966 57551 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.01 Å2
Refinement stepCycle: LAST / Resolution: 1.27→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 4 362 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621810
X-RAY DIFFRACTIONf_angle_d0.80482484
X-RAY DIFFRACTIONf_chiral_restr0.0654251
X-RAY DIFFRACTIONf_plane_restr0.0049326
X-RAY DIFFRACTIONf_dihedral_angle_d13.28721038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.290.38751450.33823823X-RAY DIFFRACTION97.14
1.29-1.30.32051540.30733932X-RAY DIFFRACTION98.6
1.3-1.320.32081190.29533873X-RAY DIFFRACTION99.35
1.32-1.340.26911420.28343908X-RAY DIFFRACTION99.39
1.34-1.360.2891470.27373928X-RAY DIFFRACTION99.8
1.36-1.380.26721560.2553884X-RAY DIFFRACTION99.78
1.38-1.40.24891270.25313947X-RAY DIFFRACTION99.78
1.4-1.430.26091440.24283951X-RAY DIFFRACTION99.98
1.43-1.450.23641490.22773917X-RAY DIFFRACTION99.98
1.45-1.480.27941450.21953946X-RAY DIFFRACTION100
1.48-1.510.22541250.21443944X-RAY DIFFRACTION100
1.51-1.540.21731570.20983917X-RAY DIFFRACTION100
1.54-1.580.25481350.2083956X-RAY DIFFRACTION100
1.58-1.620.23531370.19673919X-RAY DIFFRACTION100
1.62-1.660.25681440.20223921X-RAY DIFFRACTION99.9
1.66-1.710.24421190.19923978X-RAY DIFFRACTION100
1.71-1.770.24131660.20343905X-RAY DIFFRACTION100
1.77-1.830.1841250.2083948X-RAY DIFFRACTION99.8
1.83-1.90.2091440.2033916X-RAY DIFFRACTION99.71
1.9-1.990.22531510.20243892X-RAY DIFFRACTION99.75
1.99-2.10.18621390.1863980X-RAY DIFFRACTION99.85
2.1-2.230.19641420.18773913X-RAY DIFFRACTION99.68
2.23-2.40.18321380.1933908X-RAY DIFFRACTION99.66
2.4-2.640.21291510.19143915X-RAY DIFFRACTION99.9
2.64-3.020.20861410.18733943X-RAY DIFFRACTION99.93
3.02-3.810.19891370.16973941X-RAY DIFFRACTION99.95
3.81-34.420.17641340.16693928X-RAY DIFFRACTION99.71

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