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- PDB-8del: Trimeric Heme-Free Cytochrome Variant ApoCyt-TriCyt3 -

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Basic information

Entry
Database: PDB / ID: 8del
TitleTrimeric Heme-Free Cytochrome Variant ApoCyt-TriCyt3
ComponentsSoluble cytochrome b562
KeywordsDE NOVO PROTEIN / apo cytochrome b562 / engineered protein
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsHoffnagle, A.M. / Eng, V.H. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-12948080 United States
CitationJournal: Biochemistry / Year: 2022
Title: Computationally Guided Redesign of a Heme-free Cytochrome with Native-like Structure and Stability.
Authors: Hoffnagle, A.M. / Eng, V.H. / Markel, U. / Tezcan, F.A.
History
DepositionJun 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 12, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)35,9606
Polymers35,8463
Non-polymers1143
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Assembly determined by sedimentation velocity analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-74 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.778, 77.076, 92.653
Angle α, β, γ (deg.)90.000, 98.690, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21C-228-

HOH

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Components

#1: Protein Soluble cytochrome b562


Mass: 11948.515 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: cybC / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 1500, 200 mM (NH4)2SO4, 100 mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.56→45.8 Å / Num. obs: 9904 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.021 / Rrim(I) all: 0.0677 / Net I/σ(I): 17.2
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 981 / CC1/2: 0.926 / Rpim(I) all: 0.255 / Rrim(I) all: 0.592 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
APEXdata reduction
APEXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6wzc

6wzc


Resolution: 2.56→45.8 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.05
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2785 1901 9.86 %
Rwork0.2025 --
obs0.2102 9887 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.56→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 3 105 2625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872575
X-RAY DIFFRACTIONf_angle_d1.10273473
X-RAY DIFFRACTIONf_chiral_restr0.0558374
X-RAY DIFFRACTIONf_plane_restr0.0076456
X-RAY DIFFRACTIONf_dihedral_angle_d25.5471988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.56-2.620.36031329.50.2803125998
2.62-2.690.36311279.60.27651194100
2.69-2.770.362415610.90.26671277100
2.77-2.860.3915133100.27551201100
2.86-2.960.3371279.10.24321273100
2.96-3.080.35011359.80.25071243100
3.08-3.220.366214310.60.24351203100
3.22-3.390.2911141100.22471268100
3.39-3.610.30091339.80.19641231100
3.61-3.880.2661279.20.19031246100
3.89-4.270.26361329.50.17711252100
4.28-4.890.201514310.10.16941269100
4.9-6.160.3002149110.20071209100
6.16-45.80.187412390.1483124999

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