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- PDB-6wz2: Co-bound structure of an engineered protein trimer, TriCyt3 -

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Basic information

Entry
Database: PDB / ID: 6wz2
TitleCo-bound structure of an engineered protein trimer, TriCyt3
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / four-helix bundle / metalloprotein trimer
Function / homology
Function and homology information


electron transport chain / electron transfer activity / periplasmic space / 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: 2.0006 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
Revision 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,48112
Polymers35,3893
Non-polymers2,0929
Water3,963220
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 area7850 Å2
ΔGint-136 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.252, 78.105, 49.562
Angle α, β, γ (deg.)90.00, 106.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11796.407 Da / Num. of mol.: 3
Mutation: T31K, A35K, Q41K, D54A, K59I, H63V, I67E, V69A, G70W, Q71E, D73H, L76A, K77H, N80K, 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


Mass: 618.503 Da / Num. of mol.: 3 / 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG1500, 0.2 M MgCl2, 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2398 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.0006→35.0477 Å / Num. obs: 23044 / % possible obs: 96.62 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0596 / Rpim(I) all: 0.02456 / Rrim(I) all: 0.06459 / Net I/σ(I): 20.34
Reflection shellResolution: 2.001→2.073 Å / Rmerge(I) obs: 0.4254 / Mean I/σ(I) obs: 3.64 / Num. unique obs: 1947 / CC1/2: 0.926 / Rpim(I) all: 0.1891 / Rrim(I) all: 0.4669

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 2.0006→35.0477 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 2020 8.77 %
Rwork0.1746 --
obs0.1783 23043 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0006→35.0477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 6 220 2827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082675
X-RAY DIFFRACTIONf_angle_d0.8763632
X-RAY DIFFRACTIONf_dihedral_angle_d28.0281011
X-RAY DIFFRACTIONf_chiral_restr0.042374
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.05060.30931130.21951219X-RAY DIFFRACTION79
2.0506-2.10610.26281520.19241464X-RAY DIFFRACTION94
2.1061-2.1680.21891420.17731544X-RAY DIFFRACTION99
2.168-2.2380.20951520.16471521X-RAY DIFFRACTION99
2.238-2.3180.22051420.16561507X-RAY DIFFRACTION98
2.318-2.41070.2221430.18041489X-RAY DIFFRACTION96
2.4107-2.52040.22341470.17251545X-RAY DIFFRACTION99
2.5204-2.65330.23881460.1751530X-RAY DIFFRACTION99
2.6533-2.81940.23081440.1761529X-RAY DIFFRACTION98
2.8194-3.0370.22131480.17261503X-RAY DIFFRACTION98
3.037-3.34240.22111460.18271542X-RAY DIFFRACTION99
3.3424-3.82560.22211430.16951522X-RAY DIFFRACTION97
3.8256-4.81780.17931540.15281557X-RAY DIFFRACTION99
4.8178-35.04770.21261480.19191551X-RAY DIFFRACTION98

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