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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oyv
TitleE.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88A S247D in complex with spermidine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / E.coli / Periplasmic binding protein / PotF / Spermidine
Function / homology
Function and homology information


polyamine binding / polyamine transport / periplasmic space
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
(2~{S})-1-methoxypropan-2-amine / Chem-3IZ / (2R)-1-methoxypropan-2-amine / SPERMIDINE / Putrescine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 20, 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
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,28915
Polymers78,9652
Non-polymers1,32413
Water4,035224
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2698
Polymers39,4831
Non-polymers7877
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0207
Polymers39,4831
Non-polymers5376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.613, 122.576, 190.320
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-712-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 29 through 63 or resid 65...
d_2ens_1(chain "B" and (resid 29 through 63 or resid 65...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNASPA1 - 35
d_12ens_1ASNGLYA37 - 47
d_13ens_1THRPROA49 - 79
d_14ens_1TRPALAA81 - 102
d_15ens_1PROSERA104 - 146
d_16ens_1GLYSERA148 - 199
d_17ens_1TYRILEA201 - 210
d_18ens_1VALALAA212 - 245
d_19ens_1ALAGLNA247 - 323
d_110ens_1PROASPA325 - 328
d_111ens_1VALLYSA330 - 339
d_112ens_1GLYGLYA341
d_113ens_1J0FJ0FC
d_114ens_1J0FJ0FD
d_115ens_1SPDSPDE
d_116ens_13IE3IEF
d_21ens_1GLNASPH1 - 35
d_22ens_1ASNGLYH37 - 47
d_23ens_1THRPROH49 - 79
d_24ens_1TRPALAH81 - 102
d_25ens_1PROSERH104 - 146
d_26ens_1GLYSERH148 - 199
d_27ens_1TYRILEH201 - 210
d_28ens_1VALALAH212 - 245
d_29ens_1ALAGLNH247 - 323
d_210ens_1PROASPH325 - 328
d_211ens_1VALLYSH330 - 339
d_212ens_1GLYGLYH341
d_213ens_1J0FJ0FJ
d_214ens_1J0FJ0FK
d_215ens_1SPDSPDL
d_216ens_13IE3IEM

NCS oper: (Code: givenMatrix: (-0.992090592022, 0.00773160003784, -0.12528559208), (-0.00208090739812, -0.998977113912, -0.0451707394701), (-0.125506681281, -0.0445527579475, 0.991091885101)Vector: - ...NCS oper: (Code: given
Matrix: (-0.992090592022, 0.00773160003784, -0.12528559208), (-0.00208090739812, -0.998977113912, -0.0451707394701), (-0.125506681281, -0.0445527579475, 0.991091885101)
Vector: -5.95500579795, 11.2718658384, -0.565642505354)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putrescine-binding periplasmic protein


Mass: 39482.574 Da / Num. of mol.: 2 / Mutation: S38T, S87Y, F88A, A182D, 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, 237 molecules

#2: Chemical ChemComp-3IZ / (2~{R})-1-[(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-yl]oxypropan-2-amine


Mass: 249.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO4
#3: Chemical
ChemComp-JFN / (2R)-1-methoxypropan-2-amine / jeffamine


Mass: 89.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H11NO
#4: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-3IE / (2~{S})-1-methoxypropan-2-amine


Mass: 89.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H11NO
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.82 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 2.4 M AmSO4 + 0.1 M Bicine pH 8.3 + 4.5% Jeffamine M600

-
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 11, 2019
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: 1.9→47.58 Å / Num. obs: 62244 / % possible obs: 90.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 33.11 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.039 / Rrim(I) all: 0.128 / Net I/σ(I): 13.74
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.6 % / Rmerge(I) obs: 2.003 / Mean I/σ(I) obs: 1 / Num. unique obs: 5363 / CC1/2: 0.375 / CC star: 0.739 / Rpim(I) all: 0.712 / Rrim(I) all: 2.139 / % possible all: 79.5

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.5model building
XDS20190806data reduction
XSCALE20190806data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.9→47.58 Å / SU ML: 0.3176 / Cross valid method: FREE R-VALUE / Phase error: 31.0686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2763 2101 3.38 %
Rwork0.2273 60126 -
obs0.2289 62236 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 0 87 224 5687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675657
X-RAY DIFFRACTIONf_angle_d0.86297696
X-RAY DIFFRACTIONf_chiral_restr0.053848
X-RAY DIFFRACTIONf_plane_restr0.0067991
X-RAY DIFFRACTIONf_dihedral_angle_d17.28082091
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.71538110344 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.47341150.43343280X-RAY DIFFRACTION74.8
1.94-1.990.3971320.35063769X-RAY DIFFRACTION86.73
1.99-2.040.34391320.31393786X-RAY DIFFRACTION86.36
2.04-2.10.36481320.29443770X-RAY DIFFRACTION86.65
2.1-2.170.33341320.29923792X-RAY DIFFRACTION86.68
2.17-2.250.3541310.28423742X-RAY DIFFRACTION86.03
2.25-2.340.31731360.25633910X-RAY DIFFRACTION89.14
2.34-2.440.27421410.24374014X-RAY DIFFRACTION91.97
2.44-2.570.28051410.24384049X-RAY DIFFRACTION91.81
2.57-2.730.31781420.24354073X-RAY DIFFRACTION92.47
2.73-2.950.27011480.24464218X-RAY DIFFRACTION95.79
2.95-3.240.29871490.23074275X-RAY DIFFRACTION96.4
3.24-3.710.2441520.20624360X-RAY DIFFRACTION97.98
3.71-4.670.23691560.17894455X-RAY DIFFRACTION99.59
4.67-47.580.23721620.19674633X-RAY DIFFRACTION99.77
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)
11.23913422570.4292202725040.4822001056471.776609738730.3505605483051.45033209294-0.0801176106299-0.0904907827204-0.07532997473440.0597169417502-0.005481054586560.1495113033160.0944071072325-0.113126125567-0.002837286133840.2048217821650.0555178194640.01514696847280.253653057797-0.04178560093010.250208640864-17.488251828111.1739718771-22.5045129832
21.02028676176-0.0246626915884-0.3709171116321.58057819751-0.06435069571721.15021980409-0.0879130099415-0.04042889580340.04788531388610.006178163062410.0248004878895-0.01318178725560.0325434800990.0698623238408-3.85501994478E-50.2313567730040.0449211396457-0.04927180262710.2738312031430.00566061106370.23054179589114.36526989131.2549572984-21.1341175351
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 29 - 369 / Label seq-ID: 1 - 341

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 29 through 369)AA
22(chain 'B' and resid 29 through 369)BH

+
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