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- PDB-7n4g: Co-bound crystal structure of the engineered cyt cb562 variant, A... -

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Basic information

Entry
Database: PDB / ID: 7n4g
TitleCo-bound crystal structure of the engineered cyt cb562 variant, AB2-H100A, crystallized in the presence of Co(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 / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsChoi, T.S. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
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
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 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 1.3Oct 23, 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)24,9935
Polymers23,6972
Non-polymers1,2963
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Metal-binding was confirmed in ESI-MS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-60 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.210, 78.270, 39.000
Angle α, β, γ (deg.)90.000, 100.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11848.306 Da / Num. of mol.: 2
Mutation: K59W, D60H, I67H, Q71H, T96C, T97H, R98C, Y101C, 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.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG1500 25%, MgCl2 200 mM, 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: 1.6 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 1.93→34.6 Å / Num. obs: 15651 / % possible obs: 98.89 % / Redundancy: 13.9 % / Biso Wilson estimate: 36.53 Å2 / CC1/2: 0.82 / Rmerge(I) obs: 0.5892 / Rpim(I) all: 0.1643 / Rrim(I) all: 0.6126 / Net I/σ(I): 159.03
Reflection shellResolution: 1.93→1.999 Å / Rmerge(I) obs: 0.8141 / Mean I/σ(I) obs: 6.55 / Num. unique obs: 1535 / CC1/2: 0.83 / Rpim(I) all: 0.2242

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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: 1.93→34.6 Å / SU ML: 0.3703 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 38.965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3245 2734 9.93 %
Rwork0.264 24804 -
obs0.2701 15651 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.13 Å2
Refinement stepCycle: LAST / Resolution: 1.93→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 1 19 1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871781
X-RAY DIFFRACTIONf_angle_d1.19062432
X-RAY DIFFRACTIONf_chiral_restr0.0449244
X-RAY DIFFRACTIONf_plane_restr0.0062319
X-RAY DIFFRACTIONf_dihedral_angle_d12.81561060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.52461410.41911256X-RAY DIFFRACTION88.92
1.96-20.40191270.37531195X-RAY DIFFRACTION88.31
2-2.040.41961350.31971265X-RAY DIFFRACTION88.33
2.04-2.080.34391380.31711240X-RAY DIFFRACTION90.54
2.08-2.120.33251310.33591194X-RAY DIFFRACTION86.83
2.12-2.170.40011370.3331172X-RAY DIFFRACTION85.28
2.17-2.230.3411250.32331148X-RAY DIFFRACTION82.99
2.23-2.290.34471410.34261234X-RAY DIFFRACTION87.75
2.29-2.360.35811380.32061276X-RAY DIFFRACTION92.3
2.36-2.430.34561370.31121258X-RAY DIFFRACTION91.78
2.43-2.520.35281410.3041266X-RAY DIFFRACTION90.66
2.52-2.620.40931250.33381202X-RAY DIFFRACTION86.34
2.62-2.740.43381390.33781218X-RAY DIFFRACTION88.12
2.74-2.880.34961370.31761232X-RAY DIFFRACTION90.36
2.88-3.060.36721400.30191303X-RAY DIFFRACTION93.46
3.06-3.30.37171360.2951282X-RAY DIFFRACTION92.32
3.3-3.630.37751420.27061240X-RAY DIFFRACTION88.99
3.63-4.160.26991500.23111287X-RAY DIFFRACTION94.73
4.16-5.230.30381350.21111248X-RAY DIFFRACTION89
5.23-34.60.21991390.16951288X-RAY DIFFRACTION92.78

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