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- PDB-6wz3: Cu-bound structure of the engineered protein trimer, TriCyt3 -

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Basic information

Entry
Database: PDB / ID: 6wz3
TitleCu-bound structure of the engineered protein trimer, TriCyt3
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / four-helix bundle / metalloprotein trimer
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
COPPER (II) ION / HEME C / DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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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)37,66315
Polymers35,3893
Non-polymers2,27312
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Oligomerization state of assembly was determined via analytical ultracentrifugation (AUC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-128 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.447, 81.205, 56.431
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-203-

CL

21A-399-

HOH

31C-377-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 318 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG1500, 0.2 M MgCl2, 0.1 M BIS-TRIS (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.4855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4855 Å / Relative weight: 1
ReflectionResolution: 1.8→39.1817 Å / Num. obs: 61197 / % possible obs: 94.92 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03397 / Rpim(I) all: 0.02206 / Rrim(I) all: 0.04069 / Net I/σ(I): 22.13
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.2815 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 3241 / CC1/2: 0.891 / Rpim(I) all: 0.1948 / Rrim(I) all: 0.3442

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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: 1.8→39.1817 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 3803 6.21 %
Rwork0.1875 --
obs0.1905 61197 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.1817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 15 306 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072782
X-RAY DIFFRACTIONf_angle_d0.8013787
X-RAY DIFFRACTIONf_dihedral_angle_d27.5811091
X-RAY DIFFRACTIONf_chiral_restr0.042388
X-RAY DIFFRACTIONf_plane_restr0.004488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.82280.31661140.26672206X-RAY DIFFRACTION96
1.8228-1.84680.31411720.25092068X-RAY DIFFRACTION95
1.8468-1.87210.26941530.24792099X-RAY DIFFRACTION95
1.8721-1.89890.41181370.29852120X-RAY DIFFRACTION94
1.8989-1.92720.41281420.37022006X-RAY DIFFRACTION90
1.9272-1.95730.26531260.28492024X-RAY DIFFRACTION89
1.9573-1.98940.35371410.24461846X-RAY DIFFRACTION85
1.9894-2.02370.27061500.23172277X-RAY DIFFRACTION98
2.0237-2.06050.23641330.22962117X-RAY DIFFRACTION97
2.0605-2.10010.33811720.26082140X-RAY DIFFRACTION96
2.1001-2.1430.23161230.21022147X-RAY DIFFRACTION97
2.143-2.18960.21141320.19192151X-RAY DIFFRACTION96
2.1896-2.24050.28291680.19942100X-RAY DIFFRACTION93
2.2405-2.29660.34521180.24681786X-RAY DIFFRACTION81
2.2966-2.35860.23771060.20252247X-RAY DIFFRACTION97
2.3586-2.4280.29461210.2062168X-RAY DIFFRACTION99
2.428-2.50640.19271710.1952217X-RAY DIFFRACTION99
2.5064-2.5960.27621520.19572218X-RAY DIFFRACTION99
2.596-2.69990.25551550.18642221X-RAY DIFFRACTION97
2.6999-2.82270.20461380.18612023X-RAY DIFFRACTION91
2.8227-2.97150.23841570.17572056X-RAY DIFFRACTION93
2.9715-3.15760.19021220.17612242X-RAY DIFFRACTION99
3.1576-3.40130.22821530.1632205X-RAY DIFFRACTION99
3.4013-3.74330.21411430.15622246X-RAY DIFFRACTION99
3.7433-4.28440.21331340.15362044X-RAY DIFFRACTION92
4.2844-5.39560.2111170.16392235X-RAY DIFFRACTION99
5.3956-39.18170.16511530.15472185X-RAY DIFFRACTION98

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