[English] 日本語
Yorodumi
- PDB-4ikx: Crystal structure of peptide transporter POT (E310Q mutant) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ikx
TitleCrystal structure of peptide transporter POT (E310Q mutant)
ComponentsDi-tripeptide ABC transporter (Permease)
KeywordsTRANSPORT PROTEIN / major facilitator superfamily
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / plasma membrane
Similarity search - Function
Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; ...Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
OLEIC ACID / Di-tripeptide ABC transporter (Permease)
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDoki, S. / Kato, H.E. / Ishitani, R. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT.
Authors: Doki, S. / Kato, H.E. / Solcan, N. / Iwaki, M. / Koyama, M. / Hattori, M. / Iwase, N. / Tsukazaki, T. / Sugita, Y. / Kandori, H. / Newstead, S. / Ishitani, R. / Nureki, O.
History
DepositionDec 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Di-tripeptide ABC transporter (Permease)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4326
Polymers54,7661
Non-polymers6675
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.146, 95.239, 57.592
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Di-tripeptide ABC transporter (Permease)


Mass: 54765.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: BD53 / Gene: GK2020 / Plasmid: pCGFP-BC / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)delta-acrB / References: UniProt: Q5KYD1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM STRAIN BD53 OF GEOBACILLUS SPECIES WHOSE SEQUENCE ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM STRAIN BD53 OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT DATABASE. THE SEQUENCE CONSTRUCT IS THE SAME AS Q5KYD1_GEOKA. C-TERMINAL RESIDUES LESSGENLYFQ ARE EXPRESSION TAGS. RESIDUE 310 (E310Q) IS ENGINEERED MUTATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.34 % / Mosaicity: 1.97 °
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 41% PEG 400, 100mM ADA-NaOH, 40mM Li2SO4, pH 6.5, lipidic cubic phase, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2012
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22683 / % possible obs: 92.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.106 / Χ2: 2.025 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.342.30.34310601.414186.1
2.34-2.382.40.33610881.412188.2
2.38-2.432.40.32410881.393190.5
2.43-2.482.60.30310671.416188.6
2.48-2.532.60.30311421.531193.1
2.53-2.592.80.28611231.557191.4
2.59-2.662.90.27511171.632192.6
2.66-2.7330.24911601.643192.7
2.73-2.8130.24411351.725194.9
2.81-2.93.20.22311731.74194.1
2.9-33.30.20811561.833195.1
3-3.123.50.18211661.745195.5
3.12-3.263.90.17111702.04195.5
3.26-3.4440.14811862.051196
3.44-3.654.60.1211852.18197.5
3.65-3.935.10.09812262.281199
3.93-4.335.30.07611982.481198.8
4.33-4.954.90.077593.009160.9
4.95-6.245.80.07112332.288199.3
6.24-506.50.04712512.189198.7

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.927 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.63 / σ(F): 1.52 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 1143 5.09 %RANDOM
Rwork0.2213 ---
obs0.2229 22460 92.58 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.063 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 180.64 Å2 / Biso mean: 32.2989 Å2 / Biso min: 4.91 Å2
Baniso -1Baniso -2Baniso -3
1-6.8258 Å20 Å21.1676 Å2
2---2.5378 Å2-0 Å2
3----4.288 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 36 83 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023810
X-RAY DIFFRACTIONf_angle_d0.665193
X-RAY DIFFRACTIONf_chiral_restr0.043603
X-RAY DIFFRACTIONf_plane_restr0.003636
X-RAY DIFFRACTIONf_dihedral_angle_d12.3591293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40460.32581320.29912539267188
2.4046-2.53140.35491450.27572598274391
2.5314-2.68990.25311300.24472646277692
2.6899-2.89740.29731510.22162701285294
2.8974-3.18870.22811460.21112765291195
3.1887-3.64940.22131480.19712761290997
3.6494-4.59520.22921410.20422519266091
4.5952-29.92990.22061500.19982788293898
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)
10.38730.0295-0.21140.50760.40921.71520.0157-0.16160.06250.20490.08550.0033-0.0477-0.00910.01890.09920.02020.00340.1137-0.03130.114412.972811.462410.9395
20.979-0.14230.00911.17970.67480.5426-0.01760.04680.0215-0.0910.0258-0.0541-0.06360.086-0.0188-0.03790.0354-0.06310.0723-0.01220.060326.81435.5267-3.6422
30.4293-0.1155-0.18270.72910.12480.26220.023-0.05610.06790.12290.09130.0196-0.0303-0.02870.04030.04240.0288-0.00530.04110.01070.06816.140713.1346.0008
40.0257-0.06840.02940.1803-0.08240.036-0.1550.07360.47090.16360.144-0.38010.18190.3510.16160.3521-0.00850.02350.527-0.01560.367140.246415.303910.7774
50.8741-0.53840.64241.801-0.79742.2331-0.0301-0.0429-0.04650.0064-0.1372-0.13920.18660.34280.08380.11770.04210.01280.30290.05610.296738.998-2.78552.7785
60.9616-0.06970.30290.8355-0.23411.2731-0.1229-0.2264-0.06120.30320.0668-0.1185-0.21410.01840.02010.21950.0718-0.01090.12720.01860.096329.7196-12.074212.7975
70.9343-0.272-0.39611.17770.06731.31310.00250.0111-0.03360.01760.07960.27370.05-0.2442-0.01920.0826-0.0205-0.00490.1357-0.00810.17658.3604-8.0937-1.1881
81.0549-0.22190.08621.1992-0.52591.1652-0.02770.0008-0.0871-0.08740.04430.21930.27-0.1246-0.02950.1641-0.02970.00440.07770.00880.20615.0407-14.97242.1738
90.68930.29430.05291.1028-0.53890.6150.0263-0.06810.04440.2301-0.05440.05040.10860.2214-0.01820.18720.0036-0.00140.11960.02170.155426.6967-12.88064.5345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:51)A2 - 51
2X-RAY DIFFRACTION2chain 'A' and (resseq 52:90)A52 - 90
3X-RAY DIFFRACTION3chain 'A' and (resseq 91:211)A91 - 211
4X-RAY DIFFRACTION4chain 'A' and (resseq 212:251)A212 - 251
5X-RAY DIFFRACTION5chain 'A' and (resseq 252:280)A252 - 280
6X-RAY DIFFRACTION6chain 'A' and (resseq 281:313)A281 - 313
7X-RAY DIFFRACTION7chain 'A' and (resseq 314:363)A314 - 363
8X-RAY DIFFRACTION8chain 'A' and (resseq 364:427)A364 - 427
9X-RAY DIFFRACTION9chain 'A' and (resseq 428:493)A428 - 493

+
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