[English] 日本語
Yorodumi
- PDB-4i62: 1.05 Angstrom crystal structure of an amino acid ABC transporter ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i62
Title1.05 Angstrom crystal structure of an amino acid ABC transporter substrate-binding protein AbpA from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein, putative
KeywordsTRANSPORT PROTEIN / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES (NIAID) / NIAID / National Institute of Allergy and Infectious Diseases / alpha and beta protein / periplasmic binding protein type ii fold / putative amino acid abc transporter system substrate binding protein / l-arginine / putative membrane-anchored lipoprotein
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Amino acid ABC transporter, periplasmic amino acid-binding protein, putative / Amino acid ABC transporter, periplasmic amino acid-binding protein, putative
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsStogios, P.J. / Kudritska, M. / Wawrzak, Z. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.05 Angstrom crystal structure of an amino acid ABC transporter substrate-binding protein from Streptococcus pneumoniae Canada MDR_19A bound to L-arginine
Authors: Stogios, P.J. / Kudritska, M. / Wawrzak, Z. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Amino acid ABC transporter, periplasmic amino acid-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5474
Polymers29,3011
Non-polymers2463
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.682, 55.028, 46.673
Angle α, β, γ (deg.)90.00, 114.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Amino acid ABC transporter, periplasmic amino acid-binding protein, putative


Mass: 29300.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: SpneCM_010100008960 / Plasmid: p15Tv-Lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04MW8, UniProt: A0A0H2ZN67*PLUS
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.93 Å3/Da / Density % sol: 27.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 30% Jeffamine ED-2001 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. obs: 91003 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.5 % / Rsym value: 0.044 / Net I/σ(I): 30.58
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 4332 / Rsym value: 0.607 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WDN

1wdn


Resolution: 1.05→23.072 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1999 2.2 %random
Rwork0.1659 ---
obs0.1662 90970 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→23.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 14 337 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112051
X-RAY DIFFRACTIONf_angle_d1.4572790
X-RAY DIFFRACTIONf_dihedral_angle_d13.655831
X-RAY DIFFRACTIONf_chiral_restr0.093325
X-RAY DIFFRACTIONf_plane_restr0.008365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0502-1.07650.29491330.26575983X-RAY DIFFRACTION93
1.0765-1.10560.25631450.23316368X-RAY DIFFRACTION99
1.1056-1.13810.22291420.20596352X-RAY DIFFRACTION100
1.1381-1.17490.18671460.19256365X-RAY DIFFRACTION100
1.1749-1.21690.19611370.18236411X-RAY DIFFRACTION100
1.2169-1.26560.19271490.17596405X-RAY DIFFRACTION100
1.2656-1.32320.20731410.17086343X-RAY DIFFRACTION100
1.3232-1.39290.17051510.17136435X-RAY DIFFRACTION100
1.3929-1.48020.19261360.16466389X-RAY DIFFRACTION100
1.4802-1.59440.18471490.15596397X-RAY DIFFRACTION100
1.5944-1.75490.17381380.15566418X-RAY DIFFRACTION100
1.7549-2.00870.18981460.1576425X-RAY DIFFRACTION100
2.0087-2.53020.16241460.15436459X-RAY DIFFRACTION100
2.5302-23.07790.16171400.16066221X-RAY DIFFRACTION95
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)
11.86390.2498-0.43321.1674-0.14861.61890.0518-0.1764-0.05650.045-0.0618-0.0570.06010.02670.01310.0583-0.0079-0.01270.0574-0.00140.055814.296423.796539.7171
21.30960.6771-0.7341.4011-0.97351.6004-0.01880.0941-0.0209-0.0826-0.0148-0.02680.01740.01970.03140.06680.0067-0.01650.0626-0.00220.065125.941931.760421.7286
32.32041.1523-0.08574.4757-1.09671.80290.0210.02950.2208-0.19910.05610.4155-0.0299-0.173-0.05460.05920.0196-0.00390.1042-0.02910.06044.187926.693533.5903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 31:125
2X-RAY DIFFRACTION2chain A and resi 126:232
3X-RAY DIFFRACTION3chain A and resi 233:268

+
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