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- PDB-6x8x: Cu-bound structure of an engineered metal-dependent protein trime... -

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Basic information

Entry
Database: PDB / ID: 6x8x
TitleCu-bound structure of an engineered metal-dependent protein trimer, TriCyt1
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 / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.505 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
DepositionJun 2, 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 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7378
Polymers11,8541
Non-polymers8827
Water34219
1
A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,21024
Polymers35,5633
Non-polymers2,64721
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5960 Å2
ΔGint-82 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.172, 82.172, 48.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-202-

CU

21A-203-

CA

31A-204-

CA

41A-206-

CA

51A-317-

HOH

61A-319-

HOH

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Components

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


Mass: 11854.326 Da / Num. of mol.: 1 / Mutation: K59H, D66N, 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


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: 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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG2000, 200 mM CaCl2, 100 mM TRIS (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.505→39.8398 Å / Num. obs: 12469 / % possible obs: 99.5 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.04198 / Rpim(I) all: 0.009792 / Rrim(I) all: 0.04313 / Net I/σ(I): 53.1
Reflection shellResolution: 2.505→2.595 Å / Redundancy: 20 % / Rmerge(I) obs: 0.2077 / Num. unique obs: 2010 / CC1/2: 0.997 / Rpim(I) all: 0.04725 / Rrim(I) all: 0.2131 / % possible all: 99.9

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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: 2.505→39.8398 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3422 1278 10.25 %
Rwork0.2847 --
obs0.2909 12469 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.505→39.8398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 6 19 897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01894
X-RAY DIFFRACTIONf_angle_d1.0611219
X-RAY DIFFRACTIONf_dihedral_angle_d13.071536
X-RAY DIFFRACTIONf_chiral_restr0.048126
X-RAY DIFFRACTIONf_plane_restr0.005159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5055-2.60580.41651440.3341199X-RAY DIFFRACTION100
2.6058-2.72440.49931460.33751273X-RAY DIFFRACTION99
2.7244-2.86790.38051400.28121238X-RAY DIFFRACTION100
2.8679-3.04760.42031380.31831232X-RAY DIFFRACTION100
3.0476-3.28280.35631450.31791264X-RAY DIFFRACTION100
3.2828-3.61290.34821400.28171235X-RAY DIFFRACTION100
3.6129-4.13530.2911460.26411250X-RAY DIFFRACTION100
4.1353-5.20820.28941540.25551234X-RAY DIFFRACTION100
5.2082-39.83980.33821250.28351266X-RAY DIFFRACTION100

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