[English] 日本語
Yorodumi
- PDB-7oys: E.coli's putrescine receptor variant PotF/D (4JDF) with mutations... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oys
TitleE.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S in complex with spermidine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / E.coli / Periplasmic binding protein / PotF / Spermidine
Function / homologypolyamine binding / polyamine transport / Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / DI(HYDROXYETHYL)ETHER / SPERMIDINE / Putrescine-binding periplasmic protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsShanmugaratnam, S. / Kroeger, P. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO4022/2-3 Germany
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Fine-tuning spermidine binding modes in the putrescine binding protein PotF.
Authors: Kroger, P. / Shanmugaratnam, S. / Scheib, U. / Hocker, B.
History
DepositionJun 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,85721
Polymers39,4551
Non-polymers1,40220
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint38 kcal/mol
Surface area14150 Å2
Unit cell
Length a, b, c (Å)37.256, 78.579, 114.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Putrescine-binding periplasmic protein


Mass: 39454.566 Da / Num. of mol.: 1 / Mutation: S38T, A182D, D247S, F276W, L348Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: potF, HPE39_07830, WP7S17E04_28980 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6S5NLK9

-
Non-polymers , 6 types, 321 molecules

#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.085 M Sodium acetate pH 4.7, 0.17M Ammonium acetate, 32.5% PEG 4000, 15% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2018
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.57→39.29 Å / Num. obs: 260238 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 21.78 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.045 / Rrim(I) all: 0.108 / Net I/σ(I): 10.35
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.027 / Mean I/σ(I) obs: 0.73 / Num. unique obs: 25374 / CC1/2: 0.256 / CC star: 0.639 / Rpim(I) all: 0.943 / Rrim(I) all: 2.242 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDS20180808data reduction
XSCALE20180808data scaling
PHASER2.8.2phasing
Coot0.9.5model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.57→39.29 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / Phase error: 22.0679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 2101 4.4 %
Rwork0.174 45644 -
obs0.1755 47745 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.34 Å2
Refinement stepCycle: LAST / Resolution: 1.57→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 90 301 3086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452918
X-RAY DIFFRACTIONf_angle_d0.75083947
X-RAY DIFFRACTIONf_chiral_restr0.0495426
X-RAY DIFFRACTIONf_plane_restr0.0062507
X-RAY DIFFRACTIONf_dihedral_angle_d12.4271094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.3791340.34742905X-RAY DIFFRACTION96.97
1.6-1.640.33651370.32222984X-RAY DIFFRACTION99.24
1.64-1.690.32881390.29733014X-RAY DIFFRACTION99.62
1.69-1.740.28481380.26523005X-RAY DIFFRACTION99.75
1.74-1.80.29411390.23153010X-RAY DIFFRACTION99.75
1.8-1.860.24281390.21743036X-RAY DIFFRACTION99.91
1.86-1.930.22031390.20473021X-RAY DIFFRACTION99.78
1.93-2.020.25711390.17273005X-RAY DIFFRACTION99.15
2.02-2.130.20061390.15423036X-RAY DIFFRACTION99.91
2.13-2.260.17791400.1473031X-RAY DIFFRACTION99.75
2.26-2.440.19341410.14353070X-RAY DIFFRACTION99.78
2.44-2.680.19291400.15463047X-RAY DIFFRACTION99.25
2.68-3.070.19911420.15723089X-RAY DIFFRACTION99.78
3.07-3.870.18471440.15493115X-RAY DIFFRACTION99.42
3.87-39.290.18871510.16523276X-RAY DIFFRACTION99.51
Refinement TLS params.Method: refined / Origin x: -0.220262566702 Å / Origin y: -0.181436657298 Å / Origin z: -11.7517981805 Å
111213212223313233
T0.132938336935 Å20.00418802345235 Å2-0.0286142470522 Å2-0.133976653489 Å2-0.00556226996556 Å2--0.152842503403 Å2
L1.04801809978 °20.141710563356 °2-0.0439929014436 °2-1.34967087416 °20.820869818971 °2--1.19725231447 °2
S0.014700146255 Å °0.0667826841202 Å °-0.119278034617 Å °0.166605620381 Å °0.00276896549448 Å °-0.0604982066391 Å °0.147145345045 Å °0.053809326565 Å °0.00964478389685 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 28 through 369)

+
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