[English] 日本語
Yorodumi
- PDB-6svf: Crystal structure of the P235GK mutant of ArgBP from T. maritima -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6svf
TitleCrystal structure of the P235GK mutant of ArgBP from T. maritima
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / DOMAIN SWAPPING / MUTAGENESIS / SUBSTRATE BINDING PROTEIN
Function / homologyBacterial periplasmic substrate-binding proteins / ligand-gated monoatomic ion channel activity / 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. / membrane / ARGININE / Amino acid ABC transporter, periplasmic amino acid-binding protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVitagliano, L. / Berisio, R. / Esposito, L. / Balasco, N. / Smaldone, G. / Ruggiero, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: The non-swapped monomeric structure of the arginine-binding protein from Thermotoga maritima.
Authors: Smaldone, G. / Ruggiero, A. / Balasco, N. / Abuhammad, A. / Autiero, I. / Caruso, D. / Esposito, D. / Ferraro, G. / Gelardi, E.L.M. / Moreira, M. / Quareshy, M. / Romano, M. / Saaret, A. / ...Authors: Smaldone, G. / Ruggiero, A. / Balasco, N. / Abuhammad, A. / Autiero, I. / Caruso, D. / Esposito, D. / Ferraro, G. / Gelardi, E.L.M. / Moreira, M. / Quareshy, M. / Romano, M. / Saaret, A. / Selvam, I. / Squeglia, F. / Troisi, R. / Kroon-Batenburg, L.M.J. / Esposito, L. / Berisio, R. / Vitagliano, L.
History
DepositionSep 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6932
Polymers25,5181
Non-polymers1751
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10670 Å2
Unit cell
Length a, b, c (Å)45.720, 52.964, 95.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 25518.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0593 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ62
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: protein concentration in the range 6-10 mg/ml in a solution containing 2.0 M ammonium sulfate and 5 % (v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 30630 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.08 / Rsym value: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 2798 / Rpim(I) all: 0.227 / Rrim(I) all: 0.345 / Rsym value: 0.258

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
EVAL15data reduction
EVAL15data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GGP

6ggp


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.94 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.098
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1420 4.6 %RANDOM
Rwork0.1709 ---
obs0.173 29166 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 47.88 Å2 / Biso mean: 14.06 Å2 / Biso min: 5.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 12 355 2165
Biso mean--7.25 29.01 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021887
X-RAY DIFFRACTIONr_bond_other_d0.0020.021853
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.9852556
X-RAY DIFFRACTIONr_angle_other_deg1.0534300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.54924.33783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23715356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6251513
X-RAY DIFFRACTIONr_chiral_restr0.1320.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 93 -
Rwork0.3 1934 -
all-2027 -
obs--89.26 %

+
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