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- PDB-6wz7: Mn-bound structure of a TriCyt3 variant -

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Basic information

Entry
Database: PDB / ID: 6wz7
TitleMn-bound structure of a TriCyt3 variant
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: 2.3 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 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
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)37,83821
Polymers35,3893
Non-polymers2,44818
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Oligomerization state of the assembly was determined via analytical ultracentrifugation (AUC).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-158 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.978, 81.847, 53.385
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-204-

CA

21B-314-

HOH

31B-338-

HOH

41B-348-

HOH

51B-368-

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, N80E, E81K, 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, 269 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 4.35 Å3/Da / Density % sol: 71.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 45% MPD, 0.2 M calcium chloride, 0.1 M HEPES (pH 7.5)

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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: 2.3→35.3956 Å / Num. obs: 26625 / % possible obs: 98.27 % / Redundancy: 3.4 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.0402 / Rrim(I) all: 0.07543 / Net I/σ(I): 13.95
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.3441 / Num. unique obs: 2615 / CC1/2: 0.863 / Rpim(I) all: 0.2197 / Rrim(I) all: 0.41

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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: 2.3→35.3956 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 2030 7.62 %
Rwork0.1803 --
obs0.1832 26625 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→35.3956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 15 251 2867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072743
X-RAY DIFFRACTIONf_angle_d0.8913737
X-RAY DIFFRACTIONf_dihedral_angle_d27.9041057
X-RAY DIFFRACTIONf_chiral_restr0.043383
X-RAY DIFFRACTIONf_plane_restr0.005486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.35360.31191270.21481598X-RAY DIFFRACTION96
2.3536-2.41250.28321320.20351643X-RAY DIFFRACTION99
2.4125-2.47770.24851460.20861641X-RAY DIFFRACTION99
2.4777-2.55060.23811290.20331640X-RAY DIFFRACTION98
2.5506-2.63290.29661310.19491658X-RAY DIFFRACTION98
2.6329-2.72690.2711200.19711582X-RAY DIFFRACTION96
2.7269-2.83610.22131330.18951611X-RAY DIFFRACTION98
2.8361-2.96510.1761380.18191681X-RAY DIFFRACTION99
2.9651-3.12130.22091360.19661645X-RAY DIFFRACTION100
3.1213-3.31670.24321430.20061617X-RAY DIFFRACTION99
3.3167-3.57260.22461390.17281619X-RAY DIFFRACTION96
3.5726-3.93170.20611370.14231648X-RAY DIFFRACTION99
3.9317-4.49970.1921330.15451671X-RAY DIFFRACTION99
4.4997-5.66530.17871430.17071630X-RAY DIFFRACTION98
5.6653-35.39560.21291430.19491711X-RAY DIFFRACTION99

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