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- PDB-6wyu: Crystallographic trimer of metal-free TriCyt2 -

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Basic information

Entry
Database: PDB / ID: 6wyu
TitleCrystallographic trimer of metal-free TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / four-helix bundle / metalloprotein trimer
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transfer activity / periplasmic space / iron ion binding / heme binding / HEME C / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsTezcan, F.A. / Kakkis, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1607145 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM112584-01 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites.
Authors: Kakkis, A. / Gagnon, D. / Esselborn, J. / Britt, R.D. / Tezcan, F.A.
History
DepositionMay 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,59310
Polymers35,2873
Non-polymers2,3067
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Oligomerization state of the assembly was determined via analytical ultracentrifugation (AUC).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-133 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.258, 79.753, 50.785
Angle α, β, γ (deg.)90.00, 105.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11762.371 Da / Num. of mol.: 3
Mutation: Q41K, D54A, K59I, H63V, V69L, G70W, D73H, K77H, R98C, Y101C
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 / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 43% MPD, 0.2 M (NH4)2SO4, 0.1 M Tris (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95368 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 1.76→40.2452 Å / Num. obs: 36758 / % possible obs: 99.74 % / Redundancy: 6.3 % / CC1/2: 0.918 / Rmerge(I) obs: 0.4161 / Rpim(I) all: 0.1727 / Rrim(I) all: 0.4511 / Net I/σ(I): 3.05
Reflection shellResolution: 1.76→1.823 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.4158 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3676 / CC1/2: 0.93 / Rpim(I) all: 0.1727 / Rrim(I) all: 0.4511 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 1.76→40.2452 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 1998 5.44 %
Rwork0.1698 --
obs0.171 36758 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→40.2452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 158 293 2917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082708
X-RAY DIFFRACTIONf_angle_d0.8963695
X-RAY DIFFRACTIONf_dihedral_angle_d10.1142254
X-RAY DIFFRACTIONf_chiral_restr0.043391
X-RAY DIFFRACTIONf_plane_restr0.005470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80410.23541390.20482462X-RAY DIFFRACTION100
1.8041-1.85280.25821480.20362501X-RAY DIFFRACTION100
1.8528-1.90740.22581370.21092438X-RAY DIFFRACTION100
1.9074-1.96890.25681400.20482493X-RAY DIFFRACTION99
1.9689-2.03930.24621510.19972472X-RAY DIFFRACTION100
2.0393-2.12090.24361350.1942477X-RAY DIFFRACTION100
2.1209-2.21750.19621500.17672459X-RAY DIFFRACTION100
2.2175-2.33440.24141340.17932490X-RAY DIFFRACTION100
2.3344-2.48060.1671450.17592469X-RAY DIFFRACTION100
2.4806-2.67210.23291400.17762507X-RAY DIFFRACTION100
2.6721-2.94090.18671450.1742486X-RAY DIFFRACTION100
2.9409-3.36630.18421450.16332478X-RAY DIFFRACTION100
3.3663-4.24040.15511440.14292493X-RAY DIFFRACTION100
4.2404-40.24520.15561450.15922535X-RAY DIFFRACTION100

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