[English] 日本語
Yorodumi
- PDB-5itp: Structure of the periplasmic binding protein NocT from A.tumefaci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5itp
TitleStructure of the periplasmic binding protein NocT from A.tumefaciens in complex with octopine
ComponentsNopaline-binding periplasmic protein
KeywordsMEMBRANE PROTEIN / Periplasmic binding protein / opine
Function / homology
Function and homology information


nitrogen compound transport / ligand-gated monoatomic ion channel activity / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / 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 ...Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
octopine / DI(HYDROXYETHYL)ETHER / Nopaline-binding periplasmic protein
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVigouroux, A. / Morera, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: ISME J / Year: 2017
Title: Fitness costs restrict niche expansion by generalist niche-constructing pathogens.
Authors: Lang, J. / Vigouroux, A. / El Sahili, A. / Kwasiborski, A. / Aumont-Nicaise, M. / Dessaux, Y. / Shykoff, J.A. / Morera, S. / Faure, D.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 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: Nopaline-binding periplasmic protein
B: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,55212
Polymers58,5192
Non-polymers1,03310
Water4,630257
1
A: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,04610
Polymers29,2601
Non-polymers7879
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nopaline-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5062
Polymers29,2601
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.640, 114.640, 38.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Nopaline-binding periplasmic protein


Mass: 29259.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Gene: nocT, Atu6027, AGR_pTi_67 / Production host: Escherichia coli (E. coli) / References: UniProt: P35120
#2: Chemical ChemComp-6DB / octopine / Octopine


Mass: 246.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4K, 100 mM Tris pH 8.5 and 0.1 mM LiSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→49 Å / Num. obs: 47709 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.4 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4POX

4pox
PDB Unreleased entry


Resolution: 1.85→27.09 Å / Cor.coef. Fo:Fc: 0.9641 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.119 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2383 5 %RANDOM
Rwork0.1768 ---
obs0.1778 47656 99.75 %-
Displacement parametersBiso mean: 41.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.0485 Å20 Å20 Å2
2--1.0485 Å20 Å2
3----2.097 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: 1 / Resolution: 1.85→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 69 257 4227
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014037HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025432HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1410SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it4037HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion17.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion537SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4970SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2752 172 5.01 %
Rwork0.2629 3263 -
all0.2635 3435 -
obs--99.75 %
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)
11.03990.0485-0.441.3186-0.33511.0678-0.0191-0.00290.04220.0550.07810.215-0.0228-0.1302-0.0591-0.09220.039-0.0131-0.0764-0.0006-0.0599-16.387780.48250.1882
22.0627-0.0697-0.21291.98680.19791.3840.036-0.1438-0.04680.1035-0.09590.1491-0.13780.17980.0599-0.00980.10420.0097-0.144-0.0453-0.1515-27.9054113.544411.8312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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