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- PDB-6wz1: Mn-bound structure of an engineered protein trimer, TriCyt3 -

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Basic information

Entry
Database: PDB / ID: 6wz1
TitleMn-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 / 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: 1.999 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 1.3Oct 16, 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)37,60215
Polymers35,3893
Non-polymers2,21312
Water4,360242
1
B: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules

C: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,60215
Polymers35,3893
Non-polymers2,21312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area6490 Å2
ΔGint-131 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.759, 77.392, 47.940
Angle α, β, γ (deg.)90.00, 110.70, 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, 254 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG 400, 0.2 M CaCl2, 0.1 M BIS-TRIS (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.77114 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: 1.77114 Å / Relative weight: 1
ReflectionResolution: 1.999→34.789 Å / Num. obs: 21269 / % possible obs: 98.1 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07868 / Rpim(I) all: 0.03305 / Rrim(I) all: 0.08555 / Net I/σ(I): 18.9
Reflection shellResolution: 1.999→2.071 Å / Rmerge(I) obs: 0.2327 / Mean I/σ(I) obs: 8.26 / Num. unique obs: 2105 / CC1/2: 0.98 / Rpim(I) all: 0.09937 / Rrim(I) all: 0.2537

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 1.999→34.789 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 2006 9.43 %
Rwork0.1762 --
obs0.1812 21269 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→34.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 138 242 2852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092705
X-RAY DIFFRACTIONf_angle_d1.043681
X-RAY DIFFRACTIONf_dihedral_angle_d7.0462292
X-RAY DIFFRACTIONf_chiral_restr0.046378
X-RAY DIFFRACTIONf_plane_restr0.006476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9995-2.04950.22271410.18431346X-RAY DIFFRACTION96
2.0495-2.10490.27511450.18881384X-RAY DIFFRACTION99
2.1049-2.16680.24091440.17731370X-RAY DIFFRACTION99
2.1668-2.23670.28821510.17891372X-RAY DIFFRACTION99
2.2367-2.31660.24171310.20441345X-RAY DIFFRACTION97
2.3166-2.40940.24261470.18541379X-RAY DIFFRACTION99
2.4094-2.5190.23341440.17631397X-RAY DIFFRACTION99
2.519-2.65180.25191440.17971367X-RAY DIFFRACTION99
2.6518-2.81780.23411420.18121359X-RAY DIFFRACTION96
2.8178-3.03530.22391470.18551387X-RAY DIFFRACTION99
3.0353-3.34050.23731440.18461394X-RAY DIFFRACTION99
3.3405-3.82340.22371370.1631358X-RAY DIFFRACTION97
3.8234-4.8150.19511450.1521405X-RAY DIFFRACTION99
4.815-34.7890.20031440.17721400X-RAY DIFFRACTION98

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