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- PDB-8den: Heme-Free Cytochrome Variant ApoCyt -

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Basic information

Entry
Database: PDB / ID: 8den
TitleHeme-Free Cytochrome Variant ApoCyt
ComponentsSoluble cytochrome b562
KeywordsDE NOVO PROTEIN / apo cytochrome b562 / engineered protein
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHoffnagle, A.H. / 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
D: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)47,5774
Polymers47,5774
Non-polymers00
Water7,566420
1
A: Soluble cytochrome b562
B: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)23,7892
Polymers23,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-12 kcal/mol
Surface area10240 Å2
MethodPISA
2
C: Soluble cytochrome b562

D: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)23,7892
Polymers23,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1590 Å2
ΔGint-11 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.590, 85.880, 47.570
Angle α, β, γ (deg.)90.000, 92.490, 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: 11894.296 Da / Num. of mol.: 4
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) / References: UniProt: P0ABE7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 35.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 22% PEG 2000, 200 mM MgCl2, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2021
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.69→47.53 Å / Num. obs: 37769 / % possible obs: 95 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Χ2: 0.81 / Net I/σ(I): 10.9
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1569 / CC1/2: 0.731 / Rpim(I) all: 0.279 / Rrim(I) all: 0.689 / Χ2: 0.75 / % possible all: 76.7

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DEL

8del


Resolution: 1.69→47.53 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.99
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2166 1986 5.26 %
Rwork0.1843 --
obs0.186 37726 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.36 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.69→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 0 420 3760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673443
X-RAY DIFFRACTIONf_angle_d0.86824663
X-RAY DIFFRACTIONf_chiral_restr0.2355507
X-RAY DIFFRACTIONf_plane_restr0.0056622
X-RAY DIFFRACTIONf_dihedral_angle_d28.55061321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.69-1.740.29641245.40.2746215482
1.74-1.780.28381425.20.2589258295
1.78-1.840.3111465.80.2367236890
1.84-1.890.262813750.2237262597
1.89-1.960.26891515.40.2105262598
1.96-2.040.237813750.2077261997
2.04-2.130.2431475.30.1883261597
2.13-2.250.21161475.40.1815255696
2.25-2.390.23911385.20.1858252494
2.39-2.570.19541455.20.1854264499
2.57-2.830.20461485.40.1928261097
2.83-3.240.21641465.40.1769256495
3.24-4.080.177213650.1527259895
4.08-47.530.18821425.10.1619265697

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