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- PDB-6wz0: Fe-bound structure of an engineered metal-dependent protein trime... -

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Basic information

Entry
Database: PDB / ID: 6wz0
TitleFe-bound structure of an engineered metal-dependent protein trimer, TriCyt2
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / four-helix bundle / metalloprotein trimer
Function / homology
Function and homology information


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: 1.7 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)37,2958
Polymers35,2873
Non-polymers2,0075
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Oligomerization state was determined via analytical ultracentrifugation (AUC).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-104 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.206, 79.260, 49.916
Angle α, β, γ (deg.)90.00, 106.89, 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#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.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG400, 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: 1.7→47.7822 Å / Num. obs: 76338 / % possible obs: 98.73 % / Redundancy: 6.3 % / CC1/2: 0.91 / Rmerge(I) obs: 0.4334 / Rpim(I) all: 0.1803 / Rrim(I) all: 0.47 / Net I/σ(I): 2.94
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6 % / Rmerge(I) obs: 0.4986 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 3931 / CC1/2: 0.86 / Rpim(I) all: 0.206 / Rrim(I) all: 0.5401 / % possible all: 99.7

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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: 1.7→47.7822 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 3901 5.11 %
Rwork0.1818 --
obs0.1834 76338 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.7822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 6 270 2871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072704
X-RAY DIFFRACTIONf_angle_d0.8413692
X-RAY DIFFRACTIONf_dihedral_angle_d28.6621009
X-RAY DIFFRACTIONf_chiral_restr0.042390
X-RAY DIFFRACTIONf_plane_restr0.004476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72070.27331610.22852711X-RAY DIFFRACTION99
1.7207-1.74250.26551210.21372522X-RAY DIFFRACTION100
1.7425-1.76540.25011550.21772636X-RAY DIFFRACTION99
1.7654-1.78960.20221200.21592681X-RAY DIFFRACTION100
1.7896-1.81520.26271480.21112528X-RAY DIFFRACTION100
1.8152-1.84230.31391250.21132700X-RAY DIFFRACTION100
1.8423-1.87110.25341550.20622574X-RAY DIFFRACTION100
1.8711-1.90180.23361490.19652656X-RAY DIFFRACTION100
1.9018-1.93460.25881390.1972657X-RAY DIFFRACTION100
1.9346-1.96970.24611460.20272572X-RAY DIFFRACTION99
1.9697-2.00760.20841350.19932640X-RAY DIFFRACTION99
2.0076-2.04860.29421430.19832595X-RAY DIFFRACTION100
2.0486-2.09310.23711360.20752701X-RAY DIFFRACTION100
2.0931-2.14180.22441450.18852556X-RAY DIFFRACTION99
2.1418-2.19540.21221500.18822655X-RAY DIFFRACTION100
2.1954-2.25480.21871310.18992591X-RAY DIFFRACTION100
2.2548-2.32110.2291430.18712653X-RAY DIFFRACTION100
2.3211-2.3960.24811370.18922635X-RAY DIFFRACTION100
2.396-2.48160.22371410.18682594X-RAY DIFFRACTION99
2.4816-2.5810.20121350.17962583X-RAY DIFFRACTION99
2.581-2.69850.27091520.18432597X-RAY DIFFRACTION98
2.6985-2.84070.23411270.18372626X-RAY DIFFRACTION98
2.8407-3.01870.21991390.18122564X-RAY DIFFRACTION97
3.0187-3.25170.18741320.18632572X-RAY DIFFRACTION97
3.2517-3.57880.18411480.17432530X-RAY DIFFRACTION97
3.5788-4.09640.16051310.14992454X-RAY DIFFRACTION93
4.0964-5.16010.19071360.15662349X-RAY DIFFRACTION89
5.1601-47.78220.19381210.182305X-RAY DIFFRACTION87

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