[English] 日本語
Yorodumi
- PDB-1usk: L-leucine-binding protein with leucine bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1usk
TitleL-leucine-binding protein with leucine bound
ComponentsLEUCINE-SPECIFIC BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / LEUCINE-BINDING PROTEIN / PROTEIN STRUCTURE / ABC TRANSPORT SYSTEMS
Function / homology
Function and homology information


branched-chain amino acid transport / L-leucine binding / phenylalanine transport / isoleucine transport / valine transport / L-leucine transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LEUCINE / Leucine-specific-binding protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMagnusson, U. / Salopek-Sondi, B. / Luck, L.A. / Mowbray, S.L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: X-Ray Structures of the Leucine-Binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity
Authors: Magnusson, U. / Salopek-Sondi, B. / Luck, L.A. / Mowbray, S.L.
History
DepositionNov 25, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 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: LEUCINE-SPECIFIC BINDING PROTEIN
B: LEUCINE-SPECIFIC BINDING PROTEIN
C: LEUCINE-SPECIFIC BINDING PROTEIN
D: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,8438
Polymers148,3194
Non-polymers5254
Water3,837213
1
A: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2112
Polymers37,0801
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2112
Polymers37,0801
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2112
Polymers37,0801
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: LEUCINE-SPECIFIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2112
Polymers37,0801
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.421, 70.140, 79.902
Angle α, β, γ (deg.)112.79, 93.23, 90.97
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
LEUCINE-SPECIFIC BINDING PROTEIN / L-LEUCINE-BINDING PROTEIN / LS-BP / L-BP


Mass: 37079.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKSTY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04816
#2: Chemical
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA COMPONENT OF THE LEUCINE-SPECIFIC TRANSPORT SYSTEM, WHICH IS ONE OF TWO PERIPLASMIC BINDING ...A COMPONENT OF THE LEUCINE-SPECIFIC TRANSPORT SYSTEM, WHICH IS ONE OF TWO PERIPLASMIC BINDING PROTEIN-DEPENDENT TRANSPORT SYSTEMS OF THE HIGH-AFFINITY TRANSPORT OF THE BRANCHED-CHAIN AMINO ACIDS IN E.COLI.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.1 %
Crystal growpH: 5.6 / Details: PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
320 %PEG50001reservoir
4100 mMsodium acetate1reservoirpH4.6
50.2 Mammonium sulfate1reservoir
610 mM1reservoirCoCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.98
DetectorDate: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→38 Å / Num. obs: 72985 / % possible obs: 79.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 4.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.4 / % possible all: 22.7
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.164
Reflection shell
*PLUS
% possible obs: 22.7 % / Redundancy: 1.1 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USI

1usi


Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.129 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3702 5.1 %RANDOM
Rwork0.212 ---
obs0.214 69282 79.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20.04 Å2-0.07 Å2
2---0.04 Å21.08 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10384 0 36 213 10633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210612
X-RAY DIFFRACTIONr_bond_other_d0.0020.029496
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.95914352
X-RAY DIFFRACTIONr_angle_other_deg0.735322220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.94751376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021976
X-RAY DIFFRACTIONr_nbd_refined0.1680.21997
X-RAY DIFFRACTIONr_nbd_other0.2040.210595
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0780.26135
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3151.56828
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6210860
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.84233784
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4214.53492
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 83
Rwork0.305 1510
Refinement
*PLUS
Lowest resolution: 38 Å / Num. reflection obs: 72985 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

+
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