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- PDB-7tep: Crystal structure of a Cu-bound cytochrome cb562 variant in the p... -

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Basic information

Entry
Database: PDB / ID: 7tep
TitleCrystal structure of a Cu-bound cytochrome cb562 variant in the presence of reductant
ComponentsSoluble cytochrome b562
KeywordsMETAL BINDING PROTEIN / metalloprotein / assembly
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: 2.7 Å
AuthorsKakkis, A. / Golub, E.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM112584European Union
National Science Foundation (NSF, United States)CHE1607145European Union
European Molecular Biology Organization (EMBO)ALTF 1336-2015European Union
CitationJournal: Chem.Commun.(Camb.) / Year: 2022
Title: Redox- and metal-directed structural diversification in designed metalloprotein assemblies.
Authors: Kakkis, A. / Golub, E. / Choi, T.S. / Tezcan, F.A.
History
DepositionJan 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,35712
Polymers46,6284
Non-polymers2,7288
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, The Cu-bound assembly was characterized by sedimentation velocity ultracentrifugation (SV-AUC). Please note that the tetramer isolated in the crystal structure ...Evidence: equilibrium centrifugation, The Cu-bound assembly was characterized by sedimentation velocity ultracentrifugation (SV-AUC). Please note that the tetramer isolated in the crystal structure was not proven to exist in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-170 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.080, 80.570, 49.440
Angle α, β, γ (deg.)90.000, 102.325, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 11657.113 Da / Num. of mol.: 4
Mutation: R34A, L38A, Q41W, K42S, K59H, D66W, V69I, D73H, D74A, K77H, T96C, 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.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG1500, 0.1 M Bis-Tris, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.7→48.3 Å / Num. obs: 9592 / % possible obs: 95.88 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05709 / Rpim(I) all: 0.03648 / Rrim(I) all: 0.06803 / Net I/σ(I): 16.66
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.1458 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 900 / CC1/2: 0.953 / Rpim(I) all: 0.0941 / Rrim(I) all: 0.1742

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bc5

2bc5


Resolution: 2.7→48.3 Å / SU ML: 0.5303 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.6677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3393 1727 9.91 %
Rwork0.2534 15708 -
obs0.2619 17435 89.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 176 88 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01933599
X-RAY DIFFRACTIONf_angle_d1.99414938
X-RAY DIFFRACTIONf_chiral_restr0.0669504
X-RAY DIFFRACTIONf_plane_restr0.0111639
X-RAY DIFFRACTIONf_dihedral_angle_d22.84891312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.4241250.35481230X-RAY DIFFRACTION81.87
2.78-2.870.45741500.33651351X-RAY DIFFRACTION93.29
2.87-2.970.39771670.31351331X-RAY DIFFRACTION91.9
2.97-3.090.37751480.31271301X-RAY DIFFRACTION90.73
3.09-3.230.44351380.29411349X-RAY DIFFRACTION90.23
3.23-3.40.37351500.26591290X-RAY DIFFRACTION89.39
3.4-3.610.33111360.2371312X-RAY DIFFRACTION87.81
3.62-3.890.3381280.22991238X-RAY DIFFRACTION85.38
3.9-4.280.30621380.22341319X-RAY DIFFRACTION88.68
4.29-4.90.30641430.22791249X-RAY DIFFRACTION86.89
4.91-6.180.34851540.26861372X-RAY DIFFRACTION93.22
6.18-48.30.24051500.18871366X-RAY DIFFRACTION93.12

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