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- PDB-5yo4: Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C -

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Basic information

Entry
Database: PDB / ID: 5yo4
TitleCrystal Structure of B562RIL with engineered disulfide bond K27C-A79C
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / hemoprotein / fusion partner / helix bundle
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.37 Å
AuthorsPu, M. / Xu, Z. / Song, G. / Liu, Z.J.
CitationJournal: Protein Cell / Year: 2018
Title: Protein crystal quality oriented disulfide bond engineering.
Authors: Pu, M. / Xu, Z. / Peng, Y. / Hou, Y. / Liu, D. / Wang, Y. / Liu, H. / Song, G. / Liu, Z.J.
History
DepositionOct 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,7911
Polymers11,7911
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5880 Å2
Unit cell
Length a, b, c (Å)41.766, 51.287, 89.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

21A-343-

HOH

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Components

#1: Protein Soluble cytochrome b562 / B562RIL / Cytochrome b-562


Mass: 11791.258 Da / Num. of mol.: 1 / Mutation: M7W, H102I, R106L, K27C, A79C
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 3.2M NH4(SO4), 0.1M Bicine 2.44mM N-octanoylsucrose
PH range: 9.0-9.4

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.37→32.39 Å / Num. obs: 20635 / % possible obs: 99 % / Redundancy: 12.8 % / Net I/σ(I): 45.75

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.37→32.386 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.2125 1999 9.69 %
Rwork0.181 --
obs0.184 20633 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.37→32.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 0 152 977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008889
X-RAY DIFFRACTIONf_angle_d0.861210
X-RAY DIFFRACTIONf_dihedral_angle_d20.423350
X-RAY DIFFRACTIONf_chiral_restr0.07135
X-RAY DIFFRACTIONf_plane_restr0.004165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.369-1.40330.30011310.23151223X-RAY DIFFRACTION93
1.4033-1.44120.29951430.20441337X-RAY DIFFRACTION100
1.4412-1.48360.23971400.16971289X-RAY DIFFRACTION100
1.4836-1.53150.25051400.15671322X-RAY DIFFRACTION100
1.5315-1.58620.17931430.15711331X-RAY DIFFRACTION100
1.5862-1.64970.20821430.14431335X-RAY DIFFRACTION100
1.6497-1.72480.20371420.15571313X-RAY DIFFRACTION100
1.7248-1.81570.19561420.16011328X-RAY DIFFRACTION100
1.8157-1.92950.21451430.1671331X-RAY DIFFRACTION100
1.9295-2.07840.2131440.1741341X-RAY DIFFRACTION100
2.0784-2.28760.20291430.1591333X-RAY DIFFRACTION100
2.2876-2.61840.2111450.17691356X-RAY DIFFRACTION100
2.6184-3.29850.23251470.1891373X-RAY DIFFRACTION100
3.2985-32.39480.1951530.20811422X-RAY DIFFRACTION99

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