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- PDB-7rwv: Crystal structure of a metal-free RIDC1 variant -

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Basic information

Entry
Database: PDB / ID: 7rwv
TitleCrystal structure of a metal-free 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: 2.2 Å
AuthorsKakkis, A. / Golub, E.
Funding support United States, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 1336-2015 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM112584 United States
National Science Foundation (NSF, United States)CHE-1607145 United States
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
DepositionAug 20, 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 13, 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
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1028
Polymers46,6284
Non-polymers2,4744
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Assembly was characterized via sedimentation velocity analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-124 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.580, 92.580, 91.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 11657.113 Da / Num. of mol.: 4
Mutation: R56A, L60A, Q63W, K64S, K81H, D88W, V91I, D95H, D96A, K99H, T118C, R120C, Y123C
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG400, 0.1 M HEPES, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→46.29 Å / Num. obs: 19413 / % possible obs: 99.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 27.02 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.145 / Rrim(I) all: 0.209 / Net I/σ(I): 3.7
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1932 / CC1/2: 0.363 / Rpim(I) all: 0.523 / Rrim(I) all: 0.756 / % possible all: 99.18

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Processing

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

2bc5


Resolution: 2.2→46.29 Å / SU ML: 0.2864 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 1001 5.16 %
Rwork0.1917 18412 -
obs0.1946 19413 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 172 192 3624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01623551
X-RAY DIFFRACTIONf_angle_d1.87094867
X-RAY DIFFRACTIONf_chiral_restr0.0788495
X-RAY DIFFRACTIONf_plane_restr0.0124633
X-RAY DIFFRACTIONf_dihedral_angle_d26.3531269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.32941670.33612582X-RAY DIFFRACTION99.24
2.32-2.460.35671520.28342591X-RAY DIFFRACTION98.81
2.46-2.650.29711490.19782646X-RAY DIFFRACTION99.47
2.65-2.920.27121700.19552598X-RAY DIFFRACTION99.57
2.92-3.340.24381080.1882679X-RAY DIFFRACTION99.18
3.34-4.210.21541040.16052666X-RAY DIFFRACTION98.89
4.21-46.290.20011510.15572650X-RAY DIFFRACTION98.63

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