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- PDB-6wvf: E.coli DsbB C104S with ubiquinone -

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Basic information

Entry
Database: PDB / ID: 6wvf
TitleE.coli DsbB C104S with ubiquinone
ComponentsGreen fluorescent protein,Disulfide bond formation protein B,Green fluorescent protein
KeywordsMEMBRANE PROTEIN / Disulfide bond formation protein B(DsbB) / Disulfide bond / Disulfide oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / ubiquinone binding / protein-disulfide reductase activity / bioluminescence / generation of precursor metabolites and energy / protein folding / response to heat / electron transfer activity / plasma membrane
Similarity search - Function
Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
UBIQUINONE-1 / Disulfide bond formation protein B / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, S. / Li, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL121718 United States
Other privateForefront of Science Award United States
Other privateMCII 2020-854 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R21 EY028705 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM131008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Sci Adv / Year: 2020
Title: Termini restraining of small membrane proteins enables structure determination at near-atomic resolution.
Authors: Liu, S. / Li, S. / Yang, Y. / Li, W.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein,Disulfide bond formation protein B,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6582
Polymers45,4081
Non-polymers2501
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.381, 53.381, 280.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Green fluorescent protein,Disulfide bond formation protein B,Green fluorescent protein


Mass: 45408.066 Da / Num. of mol.: 1 / Mutation: C8A,C49V,C104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Escherichia coli (E. coli)
Gene: GFP, dsbB, roxB, ycgA, b1185, JW5182 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: P0A6M2
#2: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / Details: 34% PEG 400, 60 mM NaCl, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.68→46.23 Å / Num. obs: 13571 / % possible obs: 97.6 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.082 / Rrim(I) all: 0.203 / Net I/σ(I): 9.1 / Num. measured all: 79211 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.68-2.815.67.897894916040.2623.5078.6840.388.5
8.88-46.234.40.02819234380.9990.0140.03144.897.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.9→46.23 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 504 4.64 %
Rwork0.2588 10355 -
obs0.26 10859 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.24 Å2 / Biso mean: 113.0847 Å2 / Biso min: 57.43 Å2
Refinement stepCycle: final / Resolution: 2.9→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 18 1 3107
Biso mean--149.91 61.56 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023186
X-RAY DIFFRACTIONf_angle_d0.5014327
X-RAY DIFFRACTIONf_dihedral_angle_d20.4591142
X-RAY DIFFRACTIONf_chiral_restr0.04477
X-RAY DIFFRACTIONf_plane_restr0.004546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.190.39551180.42452502262098
3.19-3.650.35461170.34422552266998
3.65-4.60.31571290.2442575270498
4.6-46.230.23791400.22112726286697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9584-0.2232-1.6313.80060.25755.0048-0.2147-0.0552-0.27880.12850.0891-0.0059-0.02790.16450.11510.90480.0009-0.07690.6828-0.01550.4763-32.767512.6449-36.4083
24.0059-0.0643-0.20743.4247-0.66884.55860.2578-0.96410.10370.8444-0.31890.1532-0.31330.98140.00891.00790.0276-0.02981.5173-0.0120.623-22.892221.799810.9051
37.7777-1.0452-2.10823.90551.27455.9426-0.4163-0.8465-0.08620.4990.12510.2676-0.18810.16630.29480.8023-0.0202-0.12290.60810.05780.4938-36.803215.5083-30.6598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 151 )A3 - 151
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 306 )A152 - 306
3X-RAY DIFFRACTION3chain 'A' and (resid 307 through 392 )A307 - 392

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