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- PDB-5ym7: Crystal Structure of B562RIL without disulfide bond -

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Basic information

Entry
Database: PDB / ID: 5ym7
TitleCrystal Structure of B562RIL without disulfide bond
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: 1.56225177343 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 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: 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


Theoretical massNumber of molelcules
Total (without water)11,7851
Polymers11,7851
Non-polymers00
Water2,612145
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 area5940 Å2
2
A: Soluble cytochrome b562

A: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)23,5702
Polymers23,5702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area740 Å2
ΔGint-6 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.847, 51.155, 89.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

21A-336-

HOH

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Components

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


Mass: 11785.229 Da / Num. of mol.: 1 / Mutation: M7W, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / 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: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.562→44.975 Å / Num. obs: 14000 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.1521696183 Å2 / Net I/σ(I): 39.06

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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: 1.56225177343→44.975 Å / SU ML: 0.169440916656 / Cross valid method: FREE R-VALUE / σ(F): 1.3792180429 / Phase error: 21.7038281078
RfactorNum. reflection% reflection
Rfree0.238443787536 1400 10 %
Rwork0.196898359674 --
obs0.201049806393 14000 99.608680185 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.7897736626 Å2
Refinement stepCycle: LAST / Resolution: 1.56225177343→44.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 0 145 972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243368861179837
X-RAY DIFFRACTIONf_angle_d0.4587810791581129
X-RAY DIFFRACTIONf_chiral_restr0.0342376882316127
X-RAY DIFFRACTIONf_plane_restr0.0037508333394151
X-RAY DIFFRACTIONf_dihedral_angle_d21.1866755101324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5623-1.61810.2189380874151330.1993687593661191X-RAY DIFFRACTION96.2909090909
1.6181-1.68290.2589635506731380.2134477135261242X-RAY DIFFRACTION99.9275887038
1.6829-1.75950.2866604144081380.2028133809481247X-RAY DIFFRACTION100
1.7595-1.85220.2727847968151390.2080339006741251X-RAY DIFFRACTION100
1.8522-1.96830.2744924471841390.2183040586611250X-RAY DIFFRACTION100
1.9683-2.12030.2431403887161390.2045330420541248X-RAY DIFFRACTION100
2.1203-2.33360.2385742497131420.1799115962441279X-RAY DIFFRACTION100
2.3336-2.67130.2236433131381390.1992715484751256X-RAY DIFFRACTION100
2.6713-3.36530.2427577073281430.1940577461521286X-RAY DIFFRACTION100
3.3653-44.99360.218445382141500.1916622964291350X-RAY DIFFRACTION99.8003992016

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