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- PDB-5yo6: Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C -

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Basic information

Entry
Database: PDB / ID: 5yo6
TitleCrystal Structure of B562RIL with engineered disulfide bond T9C-A36C
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 / MOLECULAR REPLACEMENT / Resolution: 1.204 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 1.2Nov 22, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)11,8191
Polymers11,8191
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area5900 Å2
Unit cell
Length a, b, c (Å)41.764, 50.840, 89.685
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-423-

HOH

21A-428-

HOH

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Components

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


Mass: 11819.334 Da / Num. of mol.: 1 / Mutation: M7W, H102L. R106L, T9C, A36C
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.: 129 / 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 Å3/Da / Density % sol: 38.4 %
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: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.204→32.271 Å / Num. obs: 22730 / % possible obs: 76 % / Redundancy: 11.6 % / Biso Wilson estimate: 15.15 Å2 / Net I/σ(I): 61.49

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6T

1m6t


Resolution: 1.204→32.271 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.22
RfactorNum. reflection% reflection
Rfree0.2369 1999 8.8 %
Rwork0.2132 --
obs0.2153 22726 75.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.204→32.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 5 129 961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006850
X-RAY DIFFRACTIONf_angle_d0.851149
X-RAY DIFFRACTIONf_dihedral_angle_d21.212331
X-RAY DIFFRACTIONf_chiral_restr0.065128
X-RAY DIFFRACTIONf_plane_restr0.007153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.204-1.23420.3574180.3426178X-RAY DIFFRACTION9
1.2342-1.26750.3099450.313474X-RAY DIFFRACTION25
1.2675-1.30480.2602710.2577744X-RAY DIFFRACTION39
1.3048-1.34690.3177940.2427962X-RAY DIFFRACTION50
1.3469-1.39510.24541200.25061240X-RAY DIFFRACTION65
1.3951-1.45090.27081470.23051536X-RAY DIFFRACTION79
1.4509-1.5170.24371790.22631858X-RAY DIFFRACTION96
1.517-1.59690.22031870.22611931X-RAY DIFFRACTION100
1.5969-1.6970.25271870.21631939X-RAY DIFFRACTION100
1.697-1.8280.22791910.21971976X-RAY DIFFRACTION100
1.828-2.01190.26931850.21891926X-RAY DIFFRACTION100
2.0119-2.3030.22391900.19661980X-RAY DIFFRACTION100
2.303-2.90130.25671920.21151985X-RAY DIFFRACTION100
2.9013-32.28290.21571930.2071998X-RAY DIFFRACTION96

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