[English] 日本語
Yorodumi
- PDB-5lom: Crystal structure of the PBP SocA from Agrobacterium tumefaciens ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lom
TitleCrystal structure of the PBP SocA from Agrobacterium tumefaciens C58 in complex with DFG at 1.5 A resolution
ComponentsDeoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
KeywordsTRANSPORT PROTEIN / Periplasmic Binding Protein / Amadori compound / opine / DFG
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / periplasmic space / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Deoxyfructosylglutamine / Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMarty, L. / Vigouroux, A. / Morera, S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 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: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
B: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8247
Polymers58,0212
Non-polymers8035
Water9,170509
1
A: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4434
Polymers29,0111
Non-polymers4323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3813
Polymers29,0111
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.620, 62.030, 84.890
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein / bacterial periplasmic binding protein SocA


Mass: 29010.648 Da / Num. of mol.: 2 / Fragment: UNP residues 36-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: socA, Atu5006 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q7D447
#2: Chemical ChemComp-SNW / Deoxyfructosylglutamine / santhopine


Mass: 308.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N2O8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 1.76 Å3/Da / Density % sol: 30.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4K, 100mM Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 64331 / % possible obs: 99.2 % / Redundancy: 6.71 % / Biso Wilson estimate: 18.27 Å2 / CC1/2: 0.997 / Rsym value: 0.01 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.856 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9M

5l9m
PDB Unreleased entry


Resolution: 1.5→41.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.091 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3213 5 %RANDOM
Rwork0.191 ---
obs0.192 64244 99.4 %-
Displacement parametersBiso mean: 19.96 Å2
Baniso -1Baniso -2Baniso -3
1-3.2079 Å20 Å2-1.2138 Å2
2---4.5476 Å20 Å2
3---1.3397 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 54 509 4285
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013867HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1285SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes570HARMONIC5
X-RAY DIFFRACTIONt_it3867HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion16.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion496SEMIHARMONIC5
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_contact5272SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 233 5 %
Rwork0.329 4423 -
all0.331 4656 -
obs--98.4 %
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)
10.9180.045-0.14180.4781-0.04621.04070.0177-0.0311-0.05780.0014-0.02140.02480.0195-0.0150.0036-0.03030.0039-0.0028-0.1313-0.0036-0.0338-18.414-7.8584-46.6825
20.5217-0.0587-0.12890.4590.0110.39910.01490.0379-0.0274-0.0128-0.01590.02930-0.00980.001-0.04770.00120.0031-0.1348-0.0016-0.05-6.9548-7.5928-5.6426
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