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- PDB-6wza: Ni-bound structure of an engineered metal-dependent protein trime... -

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Basic information

Entry
Database: PDB / ID: 6wza
TitleNi-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
HEME C / NICKEL (II) ION / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Nov 6, 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)38,15921
Polymers35,5633
Non-polymers2,59618
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Oligomerization state of assembly was determined via analytical ultracentrifugation (AUC).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-211 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.115, 82.115, 137.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-307-

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: 11854.326 Da / Num. of mol.: 3 / 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

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Non-polymers , 6 types, 121 molecules

#2: Chemical ChemComp-HEC / HEME C


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


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.72 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 22.5% PEG 400, 0.2 M NaCl, 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: ALS / Beamline: 5.0.2 / Wavelength: 1.23984 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23984 Å / Relative weight: 1
ReflectionResolution: 2.5→39.3463 Å / Num. obs: 19138 / % possible obs: 99.71 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1416 / Rpim(I) all: 0.0331 / Rrim(I) all: 0.1455 / Net I/σ(I): 18.23
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.6877 / Num. unique obs: 1865 / CC1/2: 0.979 / Rpim(I) all: 0.1591 / Rrim(I) all: 0.7061

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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: 2.5→39.3463 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3059 1924 10.08 %
Rwork0.2406 --
obs0.2473 19094 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.3463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 36 103 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092723
X-RAY DIFFRACTIONf_angle_d1.0583718
X-RAY DIFFRACTIONf_dihedral_angle_d26.9531005
X-RAY DIFFRACTIONf_chiral_restr0.046385
X-RAY DIFFRACTIONf_plane_restr0.005481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.29731360.21481192X-RAY DIFFRACTION100
2.5625-2.63180.31241340.22321212X-RAY DIFFRACTION100
2.6318-2.70920.29391330.23181209X-RAY DIFFRACTION100
2.7092-2.79660.28431330.2071199X-RAY DIFFRACTION100
2.7966-2.89660.27291370.20721212X-RAY DIFFRACTION100
2.8966-3.01250.24951370.19931209X-RAY DIFFRACTION100
3.0125-3.14960.29071370.22251223X-RAY DIFFRACTION100
3.1496-3.31550.31321340.24171195X-RAY DIFFRACTION99
3.3155-3.52310.28541380.21191227X-RAY DIFFRACTION100
3.5231-3.79490.30191380.21481227X-RAY DIFFRACTION100
3.7949-4.17650.26181360.22991231X-RAY DIFFRACTION100
4.1765-4.77990.3271380.23211242X-RAY DIFFRACTION100
4.7799-6.01870.3581450.30041256X-RAY DIFFRACTION100
6.0187-39.34630.34051480.30111336X-RAY DIFFRACTION100

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