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- PDB-5yo3: Crystal Structure of B562RIL with engineered disulfide bond V16C-A29C -

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Basic information

Entry
Database: PDB / ID: 5yo3
TitleCrystal Structure of B562RIL with engineered disulfide bond V16C-A29C
ComponentsSoluble cytochrome b562
KeywordsELECTRON TRANSPORT / hemoprotein / fusion partner / helix bundle
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transfer activity / periplasmic space / iron ion binding / heme binding / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.0May 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2935
Polymers11,9081
Non-polymers3844
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-34 kcal/mol
Surface area6170 Å2
2
A: Soluble cytochrome b562
hetero molecules

A: Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,58510
Polymers23,8172
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2110 Å2
ΔGint-82 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.328, 50.126, 94.237
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-203-

SO4

21A-327-

HOH

31A-386-

HOH

41A-468-

HOH

51A-494-

HOH

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Components

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


Mass: 11908.384 Da / Num. of mol.: 1 / Mutation: M7W, V16C, A29C, H102I, R106L
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: NH4(SO4), Bicine, 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: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→47.118 Å / Num. obs: 10312 / % possible obs: 95 % / Redundancy: 4.4 % / Biso Wilson estimate: 16.76 Å2 / Net I/σ(I): 55.71
Reflection shellResolution: 1.7→1.78 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2289)refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6T

1m6t


Resolution: 1.7→47.118 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 1032 10.01 %
Rwork0.155 --
obs0.1583 10312 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 20 196 1048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003878
X-RAY DIFFRACTIONf_angle_d0.5521190
X-RAY DIFFRACTIONf_dihedral_angle_d12.21552
X-RAY DIFFRACTIONf_chiral_restr0.036132
X-RAY DIFFRACTIONf_plane_restr0.003157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.78980.26961150.19321027X-RAY DIFFRACTION75
1.7898-1.90190.2291410.17091271X-RAY DIFFRACTION93
1.9019-2.04870.21541520.1681371X-RAY DIFFRACTION100
2.0487-2.25490.18781530.14581378X-RAY DIFFRACTION100
2.2549-2.58120.16631540.151380X-RAY DIFFRACTION100
2.5812-3.25190.18271570.1511416X-RAY DIFFRACTION100
3.2519-47.13660.1781600.1521437X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 16.4812 Å / Origin y: 3.0592 Å / Origin z: -11.2233 Å
111213212223313233
T0.1102 Å20.0038 Å20.0102 Å2-0.1029 Å20.0174 Å2--0.1092 Å2
L0.6879 °20.5342 °20.7969 °2-1.5831 °21.1908 °2--1.8775 °2
S0.0027 Å °0.0024 Å °0.0077 Å °-0.0769 Å °-0.0207 Å °0.0281 Å °-0.0261 Å °-0.066 Å °0.0467 Å °
Refinement TLS groupSelection details: chain 'A' and resid 0 through 106

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