[English] 日本語
Yorodumi
- PDB-8jv3: Structure of the SAR11 PotD in complex with glycine betaine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jv3
TitleStructure of the SAR11 PotD in complex with glycine betaine
ComponentsSpermidine/putrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / PotD / substrate binding protein / solute-binding protein / periplasmic binding protein / ABC transporter system receptor / osmolyte / compatible solute / betaine / DMSP / GABA / amino acid / SAR11 / Candidatus Pelagibacter sp. HTCC7211
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / TRIMETHYL GLYCINE / Spermidine/putrescine-binding periplasmic protein
Function and homology information
Biological speciesPelagibacter sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMa, Q. / Liu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)xxxx China
CitationJournal: To Be Published
Title: Structure of the SAR11 PotD in complex with glycine betaine
Authors: Ma, Q. / Liu, C.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spermidine/putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3307
Polymers39,4431
Non-polymers8876
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.027, 78.271, 79.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Spermidine/putrescine-binding periplasmic protein


Mass: 39442.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibacter sp. (strain HTCC7211) (bacteria)
Gene: potD, PB7211_697 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: B6BQH5

-
Non-polymers , 5 types, 426 molecules

#2: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, pH7.5) and 1 ul reservoir solution (100 mM MES pH 6.5, 22% w/v mPEG 550).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.41→55.869 Å / Num. obs: 85121 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Rsym value: 0.073 / Net I/σ(I): 21.9
Reflection shellResolution: 1.41→1.434 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4225 / CC1/2: 0.783 / Rpim(I) all: 0.336 / Rrim(I) all: 1.15 / Rsym value: 1.099 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSJan 10, 2022 (BUILT 20220820)data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→26.313 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1485 4361 5.12 %random
Rwork0.1255 ---
obs0.1266 85105 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→26.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 57 420 3244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062914
X-RAY DIFFRACTIONf_angle_d1.0213946
X-RAY DIFFRACTIONf_dihedral_angle_d14.8081065
X-RAY DIFFRACTIONf_chiral_restr0.082399
X-RAY DIFFRACTIONf_plane_restr0.007506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.42560.21081240.17532690X-RAY DIFFRACTION100
1.4256-1.44240.19891470.17342632X-RAY DIFFRACTION100
1.4424-1.460.20971450.15792678X-RAY DIFFRACTION100
1.46-1.47850.17471320.14522703X-RAY DIFFRACTION100
1.4785-1.49790.17141490.13972619X-RAY DIFFRACTION100
1.4979-1.51840.16431480.13162671X-RAY DIFFRACTION100
1.5184-1.54010.17081560.12572645X-RAY DIFFRACTION100
1.5401-1.56310.17241570.11912650X-RAY DIFFRACTION100
1.5631-1.58750.1581510.11732646X-RAY DIFFRACTION100
1.5875-1.61350.16471280.10362670X-RAY DIFFRACTION100
1.6135-1.64140.1451610.10272670X-RAY DIFFRACTION100
1.6414-1.67120.14111500.10632663X-RAY DIFFRACTION100
1.6712-1.70330.15081530.10182652X-RAY DIFFRACTION100
1.7033-1.73810.12891550.10522672X-RAY DIFFRACTION100
1.7381-1.77590.12931670.10272663X-RAY DIFFRACTION100
1.7759-1.81720.13341380.10072661X-RAY DIFFRACTION100
1.8172-1.86260.13811380.10432696X-RAY DIFFRACTION100
1.8626-1.9130.13661550.11192664X-RAY DIFFRACTION100
1.913-1.96920.1581080.11542736X-RAY DIFFRACTION100
1.9692-2.03280.14991530.12042662X-RAY DIFFRACTION100
2.0328-2.10540.16131650.12142669X-RAY DIFFRACTION100
2.1054-2.18970.13551290.11972711X-RAY DIFFRACTION100
2.1897-2.28930.13821540.11572680X-RAY DIFFRACTION100
2.2893-2.40990.15571570.11482697X-RAY DIFFRACTION100
2.4099-2.56080.13231400.11892724X-RAY DIFFRACTION100
2.5608-2.75830.16511510.12742704X-RAY DIFFRACTION100
2.7583-3.03550.16871460.13532748X-RAY DIFFRACTION100
3.0355-3.47390.16321490.14532739X-RAY DIFFRACTION100
3.4739-4.37350.121230.13132812X-RAY DIFFRACTION100
4.3735-26.3130.13691320.13342917X-RAY DIFFRACTION100

+
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