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- PDB-5yo5: Crystal Structure of B562RIL with engineered disulfide bond A20C-Q25C -

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Basic information

Entry
Database: PDB / ID: 5yo5
TitleCrystal Structure of B562RIL with engineered disulfide bond A20C-Q25C
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: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562
B: Soluble cytochrome b562
C: Soluble cytochrome b562
D: Soluble cytochrome b562
E: Soluble cytochrome b562
F: Soluble cytochrome b562
G: Soluble cytochrome b562
H: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)94,9078
Polymers94,9078
Non-polymers00
Water7,062392
1
A: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,8631
Polymers11,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.665, 120.870, 95.255
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-323-

HOH

21D-233-

HOH

31D-274-

HOH

41E-316-

HOH

51F-307-

HOH

61G-308-

HOH

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Components

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


Mass: 11863.386 Da / Num. of mol.: 8 / Mutation: M7W, H102I, R106L, A20C, Q25C
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 / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.16 Å3/Da / Density % sol: 43.2 %
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: 2.2→37.7 Å / Num. obs: 79301 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.41 Å2 / Net I/σ(I): 12.35

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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: 2.2→37.7 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.94
RfactorNum. reflection% reflection
Rfree0.2673 2786 3.51 %
Rwork0.221 --
obs0.2226 79301 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6599 0 35 392 7026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086715
X-RAY DIFFRACTIONf_angle_d0.9269066
X-RAY DIFFRACTIONf_dihedral_angle_d23.0422604
X-RAY DIFFRACTIONf_chiral_restr0.0431017
X-RAY DIFFRACTIONf_plane_restr0.0071200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23790.34331110.28243196X-RAY DIFFRACTION82
2.2379-2.27860.37561100.27413508X-RAY DIFFRACTION89
2.2786-2.32250.2951460.27413641X-RAY DIFFRACTION93
2.3225-2.36990.28741420.26583815X-RAY DIFFRACTION98
2.3699-2.42140.28391320.26573940X-RAY DIFFRACTION100
2.4214-2.47770.3021570.25943832X-RAY DIFFRACTION99
2.4777-2.53960.29661280.2553885X-RAY DIFFRACTION100
2.5396-2.60830.26361440.24323959X-RAY DIFFRACTION100
2.6083-2.6850.29841480.23373877X-RAY DIFFRACTION100
2.685-2.77170.26611460.24243861X-RAY DIFFRACTION100
2.7717-2.87070.30981540.24693930X-RAY DIFFRACTION100
2.8707-2.98560.29621290.2413908X-RAY DIFFRACTION100
2.9856-3.12140.31351500.24493918X-RAY DIFFRACTION100
3.1214-3.28590.26911440.22683876X-RAY DIFFRACTION100
3.2859-3.49160.28081320.21723926X-RAY DIFFRACTION100
3.4916-3.7610.22781440.20463904X-RAY DIFFRACTION100
3.761-4.1390.25461290.1923927X-RAY DIFFRACTION100
4.139-4.7370.2681560.17813872X-RAY DIFFRACTION99
4.737-5.96430.25471560.21713869X-RAY DIFFRACTION99
5.9643-37.70620.18171280.17953871X-RAY DIFFRACTION99

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