[English] 日本語
Yorodumi
- PDB-7s7x: Crystal structure of iCytSnFR Cytisine Sensor precursor binding p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s7x
TitleCrystal structure of iCytSnFR Cytisine Sensor precursor binding protein with varenicline bound
ComponentsiNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
KeywordsFLUORESCENT PROTEIN / nicotine / gfp / periplasmic binding protein / nicotine-binding protein / fluorescent sensor / pharmacokinetic sensor / CHOLINE-BINDING PROTEIN
Function / homologyDI(HYDROXYETHYL)ETHER / VARENICLINE
Function and homology information
Biological speciesThermoanaerobacter sp. X513 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFan, C. / Nichols, N.L. / Luebbert, L. / Looger, L.L. / Lester, H.A. / Rees, D.C.
Funding support United States, 6items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA037161 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA043829 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)GM123582 United States
Tobacco-Related Disease Research Program (TRDRP)23XT-0007 United States
Tobacco-Related Disease Research Program (TRDRP)27IP-0057 United States
CitationJournal: Ph.D.Thesis,California Institute of Technology / Year: 2020
Title: Structure, Function, and Application of Bacterial ABC Transporters
Authors: Fan, C.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Structure summary / Category: struct / struct_keywords
Item: _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
B: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
C: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,67410
Polymers99,3123
Non-polymers1,3627
Water15,187843
1
A: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5223
Polymers33,1041
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6294
Polymers33,1041
Non-polymers5253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5223
Polymers33,1041
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.471, 99.910, 135.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 86 or resid 88...
21(chain C and (resid 1 through 86 or resid 88...
31(chain B and (resid 1 through 86 or resid 88...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 86 or resid 88...A1 - 86
121(chain A and (resid 1 through 86 or resid 88...A88 - 116
131(chain A and (resid 1 through 86 or resid 88...A1 - 301
141(chain A and (resid 1 through 86 or resid 88...A1 - 301
151(chain A and (resid 1 through 86 or resid 88...A123 - 156
161(chain A and (resid 1 through 86 or resid 88...A167 - 171
171(chain A and (resid 1 through 86 or resid 88...A1
181(chain A and (resid 1 through 86 or resid 88...A401
211(chain C and (resid 1 through 86 or resid 88...C1 - 86
221(chain C and (resid 1 through 86 or resid 88...C88 - 116
231(chain C and (resid 1 through 86 or resid 88...C118 - 120
241(chain C and (resid 1 through 86 or resid 88...C167 - 171
251(chain C and (resid 1 through 86 or resid 88...C9
261(chain C and (resid 1 through 86 or resid 88...C241 - 278
271(chain C and (resid 1 through 86 or resid 88...C1 - 278
281(chain C and (resid 1 through 86 or resid 88...C241 - 278
291(chain C and (resid 1 through 86 or resid 88...C301 - 401
311(chain B and (resid 1 through 86 or resid 88...B1 - 86
321(chain B and (resid 1 through 86 or resid 88...B88 - 116
331(chain B and (resid 1 through 86 or resid 88...B118 - 120
341(chain B and (resid 1 through 86 or resid 88...B123 - 156
351(chain B and (resid 1 through 86 or resid 88...B158 - 165
361(chain B and (resid 1 through 86 or resid 88...B167 - 171
371(chain B and (resid 1 through 86 or resid 88...B173 - 239
381(chain B and (resid 1 through 86 or resid 88...B241 - 278
391(chain B and (resid 1 through 86 or resid 88...B301 - 401

-
Components

#1: Protein iNicSnFR 4.0 Fluorescent Nicotine Sensor precursor binding protein


Mass: 33103.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter sp. X513 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-QMR / VARENICLINE


Mass: 211.262 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H13N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES, pH 9.5 20% PEG 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→37.92 Å / Num. obs: 96997 / % possible obs: 99.71 % / Redundancy: 2 % / Biso Wilson estimate: 20.63 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03468 / Rpim(I) all: 0.03468 / Rrim(I) all: 0.04905 / Net I/σ(I): 8.23
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4629 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 9392 / CC1/2: 0.655 / CC star: 0.89 / Rpim(I) all: 0.4629 / Rrim(I) all: 0.6546 / % possible all: 98.54

-
Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.17.1_3660refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S7T

7s7t


Resolution: 1.7→37.92 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.33
RfactorNum. reflection% reflection
Rfree0.2078 2359 2.44 %
Rwork0.1701 --
obs0.171 96851 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.23 Å2 / Biso mean: 24.4515 Å2 / Biso min: 10.27 Å2
Refinement stepCycle: final / Resolution: 1.7→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 94 843 7570
Biso mean--25.31 33.07 -
Num. residues----834
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2580X-RAY DIFFRACTION5.907TORSIONAL
12C2580X-RAY DIFFRACTION5.907TORSIONAL
13B2580X-RAY DIFFRACTION5.907TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.730.31011320.26635349548198
1.73-1.770.29211380.237954865624100
1.77-1.810.25071390.224455325671100
1.81-1.860.22111360.217254955631100
1.86-1.910.28861370.219454995636100
1.91-1.970.29131390.210755115650100
1.97-2.030.2571380.196555265664100
2.03-2.10.23551370.189155295666100
2.1-2.190.22061390.174555195658100
2.19-2.280.22971380.18355555693100
2.28-2.410.17811380.165955345672100
2.41-2.560.21331400.168655885728100
2.56-2.750.21011390.166955635702100
2.75-3.030.25451390.179956205759100
3.03-3.470.19351410.160656375778100
3.47-4.370.17371410.138956635804100
4.37-37.920.14991480.139558866034100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more