[English] 日本語
Yorodumi
- PDB-3ksx: The alkanesulfonate-binding protein SsuA from Xanthomonas axonopo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ksx
TitleThe alkanesulfonate-binding protein SsuA from Xanthomonas axonopodis pv. citri bound to MOPS
ComponentsNitrate transport protein
KeywordsTRANSPORT PROTEIN / SsuA / alkanesulfonate-binding protein / periplasmic-binding protein
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / periplasmic space / membrane
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #20 / Aliphatic sulfonates-binding protein / SsuA/THI5-like / NMT1/THI5 like / Helicase, Ruva Protein; domain 3 / Bacterial periplasmic substrate-binding proteins / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / Helix non-globular / Special ...Helicase, Ruva Protein; domain 3 - #20 / Aliphatic sulfonates-binding protein / SsuA/THI5-like / NMT1/THI5 like / Helicase, Ruva Protein; domain 3 / Bacterial periplasmic substrate-binding proteins / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / Helix non-globular / Special / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nitrate transport protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBalan, A. / Araujo, F.T. / Barbosa, J.A.R.G.
CitationJournal: To be Published
Title: The crystallographic structure of the SsuA protein reveals how alkanesulfonates enter into the cell
Authors: Balan, A. / Araujo, F.T. / Barbosa, J.A.R.G.
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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: Nitrate transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0645
Polymers34,5671
Non-polymers4974
Water3,783210
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.042, 86.446, 47.015
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nitrate transport protein


Mass: 34566.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: ssuA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PHQ1
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1.81 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 M MOPS pH 6.8, 0.1 M NaCl, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.7→26.14 Å / Num. obs: 26985 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1 % / Rmerge(I) obs: 0.1625 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1 % / % possible all: 96.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.03 Å26.14 Å
Translation2.03 Å26.14 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E4R

3e4r


Resolution: 1.7→26.14 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.722 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21303 1128 5 %RANDOM
Rwork0.1631 ---
obs0.16579 22426 83.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 28 210 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9863100
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76322.67486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0341519
X-RAY DIFFRACTIONr_chiral_restr0.1350.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211702
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.51445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01722307
X-RAY DIFFRACTIONr_scbond_it3.6723826
X-RAY DIFFRACTIONr_scangle_it5.854.5792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 34 -
Rwork0.288 701 -
obs--36.99 %

+
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