[English] 日本語
Yorodumi
- PDB-2q9t: High-resolution structure of the DING protein from Pseudomonas fl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q9t
TitleHigh-resolution structure of the DING protein from Pseudomonas fluorescens
ComponentsDING
KeywordsUNKNOWN FUNCTION / DING protein / phosphate-binding / Venus flytrap fold / PstS protein
Function / homology
Function and homology information


phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / hydrolase activity
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / PBP superfamily domain / PBP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Phosphate-binding protein PstS / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMoniot, S. / Ahn, S. / Elias, M. / Kim, D. / Scott, K. / Chabriere, E.
CitationJournal: Febs Lett. / Year: 2007
Title: Structure-function relationships in a bacterial DING protein.
Authors: Ahn, S. / Moniot, S. / Elias, M. / Chabriere, E. / Kim, D. / Scott, K.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The sequence of this protein in not available in the UNP database at the time of ...sequence The sequence of this protein in not available in the UNP database at the time of processing. The C-terminal six His residues are cloning artifacts.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,78512
Polymers38,9771
Non-polymers80811
Water13,799766
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.728, 123.679, 40.833
Angle α, β, γ (deg.)90.00, 116.71, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DING


Mass: 38977.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal hexahistidine tag / Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SBW 25 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4KD17, UniProt: D0VWY2*PLUS

-
Non-polymers , 6 types, 777 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24% PEG 8000, 100 mM acetate buffer pH 4.5, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 1.43→61.9 Å / Num. all: 60045 / Num. obs: 59063 / % possible obs: 98.1 % / Redundancy: 4 % / Biso Wilson estimate: 8.9 Å2 / Rsym value: 0.026 / Net I/σ(I): 38.9
Reflection shellResolution: 1.43→1.5 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 10.52 / Num. unique all: 7166 / Rsym value: 0.102 / % possible all: 89.2

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Phosphate-binding protein (HPBP) PDB code 2cap

2cap
PDB Unreleased entry


Resolution: 1.43→61.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.818 / SU ML: 0.034 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 2954 5 %RANDOM
Rwork0.131 ---
obs0.133 59063 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.19 Å2
2---0.26 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.43→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 49 766 3513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223067
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.954245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41625.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26915431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.151510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022404
X-RAY DIFFRACTIONr_nbd_refined0.20.21668
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2638
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.2100
X-RAY DIFFRACTIONr_mcbond_it0.5531.52040
X-RAY DIFFRACTIONr_mcangle_it0.86923284
X-RAY DIFFRACTIONr_scbond_it1.20631132
X-RAY DIFFRACTIONr_scangle_it1.6874.5928
X-RAY DIFFRACTIONr_rigid_bond_restr0.61733172
X-RAY DIFFRACTIONr_sphericity_free2.1553768
X-RAY DIFFRACTIONr_sphericity_bonded1.5132975
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 190 -
Rwork0.149 3597 -
obs-3787 100 %

+
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://pdbjlvh1.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