[English] 日本語
Yorodumi
- PDB-4la9: Crystal structure of an empty substrate binding domain 1 (SBD1) O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4la9
TitleCrystal structure of an empty substrate binding domain 1 (SBD1) OF ABC TRANSPORTER GLNPQ from lactococcus lactis
ComponentsGlutamine ABC transporter permease and substrate binding protein protein
KeywordsTRANSPORT PROTEIN / GLUTAMINE BINDING PROTEIN / AMINO ACID TRANSPORT / EXTRACELLULAR
Function / homology
Function and homology information


peptide transport / ATP-binding cassette (ABC) transporter complex / ligand-gated ion channel activity / protein transport
Similarity search - Function
Amino acid ABC transporter, permease protein, 3-TM domain / Bacterial extracellular solute-binding proteins, family 3 signature. / Solute-binding protein family 3, conserved site / ABC transporter integral membrane type-1 domain profile. / Binding-protein-dependent transport system inner membrane component / MetI-like superfamily / ABC transporter type 1, transmembrane domain MetI-like / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF ...Amino acid ABC transporter, permease protein, 3-TM domain / Bacterial extracellular solute-binding proteins, family 3 signature. / Solute-binding protein family 3, conserved site / ABC transporter integral membrane type-1 domain profile. / Binding-protein-dependent transport system inner membrane component / MetI-like superfamily / ABC transporter type 1, transmembrane domain MetI-like / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Ionotropic glutamate receptor / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glutamine ABC transporter permease and substrate binding protein protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGuskov, A. / Schuurman-Wolters, G.K. / Slotboom, D.J. / Poolman, B.
CitationJournal: Structure / Year: 2013
Title: Functional Diversity of Tandem Substrate-Binding Domains in ABC Transporters from Pathogenic Bacteria.
Authors: Fulyani, F. / Schuurman-Wolters, G.K. / Zagar, A.V. / Guskov, A. / Slotboom, D.J. / Poolman, B.
History
DepositionJun 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamine ABC transporter permease and substrate binding protein protein
B: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,17110
Polymers55,3332
Non-polymers8388
Water10,971609
1
A: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4098
Polymers27,6671
Non-polymers7437
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamine ABC transporter permease and substrate binding protein protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7622
Polymers27,6671
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.090, 55.500, 56.010
Angle α, β, γ (deg.)93.35, 92.92, 97.50
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Glutamine ABC transporter permease and substrate binding protein protein


Mass: 27666.600 Da / Num. of mol.: 2 / Fragment: SUBSTRATE BINDING DOMAIN 1, UNP residues 1-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IL1403 / Gene: glnP, L165, LL1759 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CES5
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 40% PEG600, 100 mM Sodium phosphate dibasic/Citric acid, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 281K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.3→35 Å / Num. obs: 91547 / % possible obs: 89.12 % / Observed criterion σ(F): 2
Reflection shellResolution: 1.3→1.3147 Å / % possible all: 87.5

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.729 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4578 5 %RANDOM
Rwork0.156 ---
obs0.1579 91547 89.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→34.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 54 609 4112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093615
X-RAY DIFFRACTIONf_angle_d1.2274865
X-RAY DIFFRACTIONf_dihedral_angle_d13.8381338
X-RAY DIFFRACTIONf_chiral_restr0.073523
X-RAY DIFFRACTIONf_plane_restr0.006622
LS refinement shellResolution: 1.3→1.3147 Å
RfactorNum. reflection% reflection
Rfree0.3262 148 -
Rwork0.2948 2816 -
obs--88 %

+
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