[English] 日本語
Yorodumi
- PDB-3tuj: Inward facing conformations of the MetNI methionine ABC transport... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tuj
TitleInward facing conformations of the MetNI methionine ABC transporter: DM crystal form
Components
  • D-methionine transport system permease protein metI
  • Methionine import ATP-binding protein MetN
KeywordsHYDROLASE/TRANSPORT PROTEIN / ABC-TRANSPORTER / TYPE I ABC TYPE IMPORTER / METHIONINE UPTAKE TRANSPORTER / MEMBRANE PROTEIN / AMINO-ACID TRANSPORT / ATP-BINDING / HYDROLASE / INNER MEMBRANE / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


L-methionine transmembrane transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / ABC-type D-methionine transporter activity / D-methionine transmembrane transport / methionine transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...L-methionine transmembrane transporter activity / methionine import across plasma membrane / methionine-importing ABC transporter complex / ABC-type methionine transporter / ABC-type D-methionine transporter activity / D-methionine transmembrane transport / methionine transport / Gram-negative-bacterium-type cell wall / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / : / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / MetI-like fold / MetI-like / : ...ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria / NIL domain / : / NIL domain / Methionine import ATP-binding protein metN family profile. / NIL / Methionine import ATP-binding protein MetN, ATP-binding domain / MetI-like fold / MetI-like / : / ACT domain / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ACT-like domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Methionine import ATP-binding protein MetN / D-methionine transport system permease protein MetI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsJohnson, E. / Nguyen, P. / Rees, D.C.
CitationJournal: Protein Sci. / Year: 2012
Title: Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition.
Authors: Johnson, E. / Nguyen, P.T. / Yeates, T.O. / Rees, D.C.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-methionine transport system permease protein metI
B: D-methionine transport system permease protein metI
C: Methionine import ATP-binding protein MetN
D: Methionine import ATP-binding protein MetN


Theoretical massNumber of molelcules
Total (without water)129,4484
Polymers129,4484
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-48 kcal/mol
Surface area50580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.750, 164.130, 212.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein D-methionine transport system permease protein metI


Mass: 23738.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0198, JW0194, metI, yaeE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P31547
#2: Protein Methionine import ATP-binding protein MetN


Mass: 40985.348 Da / Num. of mol.: 2 / Mutation: E166Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: abc, b0199, JW0195, metN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*
References: UniProt: P30750, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.23 Å3/Da / Density % sol: 76.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.5mM TCEP, 0.1M sodium chloride, 0.1M magnesium chloride, 0.1M HEPES, pH 7.5, 33% v/v polyethylene glycol 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 15, 2010
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionRedundancy: 16.5 % / Av σ(I) over netI: 4.5 / Number: 427428 / Rsym value: 0.11 / D res high: 3.85 Å / D res low: 129.791 Å / Num. obs: 25904 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
12.1719.8577.210.0430.04314.6
8.6112.1710010.0460.04615.3
7.038.6110010.0610.06115.9
6.097.0310010.1290.12916.4
5.446.0910010.220.2216.6
4.975.4410010.2780.27816.7
4.64.9710010.310.3116.7
4.34.610010.4590.45916.7
4.064.310010.9710.97116.8
3.854.0610012.0512.05116.8
ReflectionResolution: 3.85→129.791 Å / Num. all: 25904 / Num. obs: 25904 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 16.5 % / Rsym value: 0.11 / Net I/σ(I): 14.3
Reflection shell

Rmerge(I) obs: 0.021 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.85-4.0616.80.46318137610.02051100
4.06-4.316.80.86015335800.971100
4.3-4.616.71.65600133440.459100
4.6-4.9716.72.45241831330.31100
4.97-5.4416.72.64824928910.278100
5.44-6.0916.63.34348526200.22100
6.09-7.0316.45.53837023360.129100
7.03-8.6115.99.83175119960.061100
8.61-12.1715.312.22378515570.046100
12.17-19.85214.613.6100356860.04377.2

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
PHASEREP/MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→19.852 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7853 / SU ML: 1.64 / σ(F): 1.9 / Phase error: 28.21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 1664 7.35 %random
Rwork0.2593 ---
obs0.2618 22647 98.05 %-
all-23097 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 93.535 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 317.95 Å2 / Biso mean: 190.6678 Å2 / Biso min: 107.69 Å2
Baniso -1Baniso -2Baniso -3
1-5.197 Å2-0 Å2-0 Å2
2---5.0594 Å2-0 Å2
3----0.1376 Å2
Refinement stepCycle: LAST / Resolution: 4→19.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8559 0 0 0 8559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138705
X-RAY DIFFRACTIONf_angle_d1.28811837
X-RAY DIFFRACTIONf_chiral_restr0.0661447
X-RAY DIFFRACTIONf_plane_restr0.0091497
X-RAY DIFFRACTIONf_dihedral_angle_d12.5533181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4-4.11670.39131240.3481354147879
4.1167-4.24830.39551510.36011704185598
4.2483-4.39860.32981510.336117531904100
4.3986-4.57260.32921470.289217781925100
4.5726-4.7780.31561230.257117531876100
4.778-5.0260.31291240.254217931917100
5.026-5.33520.31451540.278417711925100
5.3352-5.73790.34231260.292718011927100
5.7379-6.29850.26741540.282817581912100
6.2985-7.1720.31191440.267817961940100
7.172-8.89840.20881250.191518361961100
8.8984-19.85180.27711410.235618862027100

+
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