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- PDB-7n4f: Ni-bound crystal structure of the engineered cyt cb562 variant, A... -

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Basic information

Entry
Database: PDB / ID: 7n4f
TitleNi-bound crystal structure of the engineered cyt cb562 variant, AB2-H100A, 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: 1.8 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)24,9925
Polymers23,6972
Non-polymers1,2963
Water1,33374
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 area3200 Å2
ΔGint-59 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.470, 84.650, 39.140
Angle α, β, γ (deg.)90.000, 100.510, 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG1500 25%, MgCl2 200 mM, pH 7 MOPS 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: May 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.59 Å / Relative weight: 1
ReflectionResolution: 1.8→35.03 Å / Num. obs: 20432 / % possible obs: 96.31 % / Redundancy: 11.9 % / Biso Wilson estimate: 25.88 Å2 / CC1/2: 0.749 / Rmerge(I) obs: 0.5845 / Rpim(I) all: 0.1812 / Rrim(I) all: 0.6132 / Net I/σ(I): 271.29
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.5606 / Mean I/σ(I) obs: 19.4 / Num. unique obs: 1985 / CC1/2: 0.817 / Rpim(I) all: 0.1773 / Rrim(I) all: 0.5889 / % possible all: 96.6

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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: 1.8→35.03 Å / SU ML: 0.2715 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 28.8039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2537 3329 9.97 %
Rwork0.2078 30068 -
obs0.2124 20432 82.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 1 74 1785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761772
X-RAY DIFFRACTIONf_angle_d0.92732428
X-RAY DIFFRACTIONf_chiral_restr0.0421246
X-RAY DIFFRACTIONf_plane_restr0.0045320
X-RAY DIFFRACTIONf_dihedral_angle_d12.87771434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.34441400.30771282X-RAY DIFFRACTION82.92
1.83-1.850.35461290.28421219X-RAY DIFFRACTION81.85
1.85-1.880.34071270.28831143X-RAY DIFFRACTION74.93
1.88-1.910.33471210.26271123X-RAY DIFFRACTION74.45
1.91-1.950.39831230.25991095X-RAY DIFFRACTION71.69
1.95-1.980.34091420.24881210X-RAY DIFFRACTION80.67
1.98-2.020.31281470.25551310X-RAY DIFFRACTION86.73
2.02-2.060.2941470.23571317X-RAY DIFFRACTION87.4
2.06-2.110.31091420.25571333X-RAY DIFFRACTION88.32
2.11-2.150.30331500.23131304X-RAY DIFFRACTION84.34
2.15-2.210.27811310.21891153X-RAY DIFFRACTION79.95
2.21-2.270.32541190.24191129X-RAY DIFFRACTION72.26
2.27-2.330.30861250.25041152X-RAY DIFFRACTION77.35
2.33-2.410.26311480.22871300X-RAY DIFFRACTION85.78
2.41-2.50.25551500.22731355X-RAY DIFFRACTION89.32
2.5-2.60.28481490.22271392X-RAY DIFFRACTION90.17
2.6-2.710.32641450.23221281X-RAY DIFFRACTION87.59
2.71-2.860.26561390.23181253X-RAY DIFFRACTION82.08
2.86-3.040.25811370.22661174X-RAY DIFFRACTION77.53
3.04-3.270.28851450.22231334X-RAY DIFFRACTION88.46
3.27-3.60.26091460.21121335X-RAY DIFFRACTION87.84
3.6-4.120.211350.17261258X-RAY DIFFRACTION83.87
4.12-5.190.18321380.15341261X-RAY DIFFRACTION82.54
5.19-35.030.16011540.14641355X-RAY DIFFRACTION89.77

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