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- PDB-7su2: Crystal structure of a Co-bound RIDC1 variant -

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Basic information

Entry
Database: PDB / ID: 7su2
TitleCrystal structure of a Co-bound RIDC1 variant
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN
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: 2 Å
AuthorsGolub, E. / Kakkis, A.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM112584European Union
National Science Foundation (NSF, United States)CHE1607145European Union
European Molecular Biology Organization (EMBO)ALTF 1336-2015European Union
CitationJournal: Chem.Commun.(Camb.) / Year: 2022
Title: Redox- and metal-directed structural diversification in designed metalloprotein assemblies.
Authors: Kakkis, A. / Golub, E. / Choi, T.S. / Tezcan, F.A.
History
DepositionNov 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.3Nov 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

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Assembly

Deposited unit
D: Soluble cytochrome b562
A: Soluble cytochrome b562
C: Soluble cytochrome b562
G: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,33812
Polymers46,6284
Non-polymers2,7108
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Oligomerization state was characterized in solution using sedimentation velocity analytical ultracentrifugation (SV-AUC).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-134 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.875, 90.024, 52.042
Angle α, β, γ (deg.)90.000, 95.907, 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: 11657.113 Da / Num. of mol.: 4
Mutation: A56, A60, W63, S64, H81, W88, I91, H95, A96, H99, C118, C120, C123
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.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CO / COBALT (II) ION


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG400, 200 mM NaCl, 100 mM HEPES (7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2→37 Å / Num. obs: 58467 / % possible obs: 98.42 % / Redundancy: 2 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01685 / Rpim(I) all: 0.01685 / Rrim(I) all: 0.02383 / Net I/σ(I): 26.68
Reflection shellResolution: 2→2.069 Å / Rmerge(I) obs: 0.05929 / Mean I/σ(I) obs: 7.4 / Num. unique obs: 5607 / CC1/2: 0.989 / Rpim(I) all: 0.05929 / Rrim(I) all: 0.08385 / % possible all: 96.01

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 2→37 Å / SU ML: 0.2535 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.4492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 3941 6.84 %
Rwork0.1839 53640 -
obs0.1871 57581 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.95 Å2
Refinement stepCycle: LAST / Resolution: 2→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 176 198 3634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313623
X-RAY DIFFRACTIONf_angle_d1.82284974
X-RAY DIFFRACTIONf_chiral_restr0.0836506
X-RAY DIFFRACTIONf_plane_restr0.0091644
X-RAY DIFFRACTIONf_dihedral_angle_d17.079496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.30041160.24891705X-RAY DIFFRACTION90.19
2.02-2.050.32471500.22461918X-RAY DIFFRACTION98.66
2.05-2.070.2571390.22341981X-RAY DIFFRACTION98.51
2.07-2.10.29921450.22081859X-RAY DIFFRACTION98.72
2.1-2.130.31871560.21591875X-RAY DIFFRACTION98.69
2.13-2.160.29131460.19882026X-RAY DIFFRACTION98.55
2.16-2.20.3081380.20031868X-RAY DIFFRACTION98.96
2.2-2.230.3141230.20771873X-RAY DIFFRACTION96.94
2.23-2.270.26191380.21311954X-RAY DIFFRACTION97.03
2.27-2.310.26151620.21661906X-RAY DIFFRACTION99.38
2.31-2.360.2881180.23021920X-RAY DIFFRACTION99.41
2.36-2.410.28571570.21051945X-RAY DIFFRACTION99.29
2.41-2.460.28921430.21861916X-RAY DIFFRACTION99.47
2.46-2.520.2571530.20331936X-RAY DIFFRACTION98.82
2.52-2.580.23241270.2151954X-RAY DIFFRACTION99.14
2.58-2.650.27521350.20611950X-RAY DIFFRACTION98.58
2.65-2.730.23261580.19881854X-RAY DIFFRACTION96.92
2.73-2.820.23491270.20051946X-RAY DIFFRACTION97.46
2.82-2.920.28721490.20621915X-RAY DIFFRACTION99.18
2.92-3.030.24781390.19641911X-RAY DIFFRACTION99.27
3.03-3.170.28891240.22011948X-RAY DIFFRACTION99.04
3.17-3.340.22381520.19971930X-RAY DIFFRACTION99.43
3.34-3.550.25561370.17771934X-RAY DIFFRACTION98.48
3.55-3.820.18221410.15381887X-RAY DIFFRACTION97.88
3.82-4.20.2031500.15031931X-RAY DIFFRACTION99.57
4.2-4.810.16711380.14051972X-RAY DIFFRACTION99.34
4.81-6.060.20051410.16161896X-RAY DIFFRACTION98.07
6.06-370.13671390.1361930X-RAY DIFFRACTION98.57

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