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- PDB-6x7e: Co-bound structure of an engineered protein trimer, TriCyt3, with... -

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Basic information

Entry
Database: PDB / ID: 6x7e
TitleCo-bound structure of an engineered protein trimer, TriCyt3, with delta isomerism at the hexahistidine coordination site
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
: / HEME C / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9987 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 29, 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 1.3Oct 23, 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)37,52015
Polymers35,3893
Non-polymers2,13112
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Oligomeric state was determined via analytical ultracentrifugation (AUC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-119 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.090, 78.003, 50.189
Angle α, β, γ (deg.)90.00, 106.48, 90.00
Int Tables number4
Space group name H-MP1211

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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, 385 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.52 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG1500, 200 mM MgCl2, 100 mM TRIS (8.5)

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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 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4855 Å / Relative weight: 1
ReflectionResolution: 1.9987→39.7039 Å / Num. obs: 23245 / % possible obs: 96.31 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0418 / Rpim(I) all: 0.02655 / Rrim(I) all: 0.04973 / Net I/σ(I): 23.76
Reflection shellResolution: 1.999→2.071 Å / Rmerge(I) obs: 0.09344 / Mean I/σ(I) obs: 9.79 / Num. unique obs: 2169 / CC1/2: 0.99 / Rpim(I) all: 0.06061 / Rrim(I) all: 0.1119 / % possible all: 90.83

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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: 1.9987→39.7039 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 2009 8.64 %
Rwork0.1615 --
obs0.1659 23245 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9987→39.7039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 9 373 2983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072709
X-RAY DIFFRACTIONf_angle_d0.9163681
X-RAY DIFFRACTIONf_dihedral_angle_d6.852285
X-RAY DIFFRACTIONf_chiral_restr0.041378
X-RAY DIFFRACTIONf_plane_restr0.005474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9987-2.04870.25741300.18221394X-RAY DIFFRACTION88
2.0487-2.10410.23871370.17371506X-RAY DIFFRACTION96
2.1041-2.1660.2371410.16641503X-RAY DIFFRACTION96
2.166-2.23590.2381500.16371505X-RAY DIFFRACTION97
2.2359-2.31580.22521250.1661514X-RAY DIFFRACTION96
2.3158-2.40850.22381520.17141532X-RAY DIFFRACTION98
2.4085-2.51810.23491440.17271521X-RAY DIFFRACTION97
2.5181-2.65090.20951490.16281544X-RAY DIFFRACTION98
2.6509-2.81690.21091430.17361494X-RAY DIFFRACTION96
2.8169-3.03430.21651540.16011511X-RAY DIFFRACTION98
3.0343-3.33950.23351430.16841545X-RAY DIFFRACTION98
3.3395-3.82240.17991480.14871528X-RAY DIFFRACTION97
3.8224-4.81450.18091470.13861579X-RAY DIFFRACTION99
4.8145-39.70390.21351460.16831560X-RAY DIFFRACTION97

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