[English] 日本語
Yorodumi
- PDB-1gub: Hinge-bending motion of D-allose binding protein from Escherichia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gub
TitleHinge-bending motion of D-allose binding protein from Escherichia coli: three open conformations
ComponentsD-ALLOSE-BINDING PERIPLASMIC PROTEIN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / ALLOSE / HINGE BENDING / CONFORMATIONAL CHANGE
Function / homology
Function and homology information


D-allose transmembrane transport / D-ribose transmembrane transport / monosaccharide binding / transmembrane transport / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / D-allose-binding periplasmic protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMagnusson, U. / Chaudhuri, B.N. / Ko, J. / Park, C. / Jones, T.A. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure of D-Allose Binding Protein from Escherichia Coli Bound to D-Allose at 1.8 A Resolution
Authors: Chaudhuri, B.N. / Ko, J. / Park, C. / Jones, T.A. / Mowbray, S.L.
#1: Journal: J.Bacteriol. / Year: 1997
Title: The D-Allose Operon of Escherichia Coli K-12
Authors: Kim, C. / Song, S. / Park, C.
History
DepositionJan 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-ALLOSE-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4772
Polymers30,4181
Non-polymers591
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.100, 133.100, 133.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

-
Components

#1: Protein D-ALLOSE-BINDING PERIPLASMIC PROTEIN / ALBP


Mass: 30417.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12 / References: UniProt: P39265
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.23 Å3/Da / Density % sol: 62 %
Crystal growpH: 9 / Details: pH 9.00
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
15 mg/mlprotein1drop
210 mMHEPES1droppH7.8
320-30 %PEG2000MME1reservoir
40.1 MTris-HCl1reservoirpH9.0
50.01 M1reservoirNiCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.89
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.08→29 Å / Num. obs: 625 / % possible obs: 99.5 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.0094 / Net I/σ(I): 7.1
Reflection shellResolution: 3.08→3.16 Å / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 29 Å / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.338

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPJ

1rpj


Resolution: 3.1→29.75 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.781 / SU B: 27.453 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.589 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.339 550 7.1 %RANDOM
Rwork0.28 ---
obs0.284 7191 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.37 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 1 10 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0740.0222161
X-RAY DIFFRACTIONr_bond_other_d0.0420.022016
X-RAY DIFFRACTIONr_angle_refined_deg3.291.9662921
X-RAY DIFFRACTIONr_angle_other_deg2.41434715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3580.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022422
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02377
X-RAY DIFFRACTIONr_nbd_refined0.2310.2482
X-RAY DIFFRACTIONr_nbd_other0.2310.22351
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1220.21476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.8860.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.6280.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.3671.51425
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it12.19122274
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3383736
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9414.5647
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 30
Rwork0.286 515
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 29 Å / Num. reflection obs: 7260 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.5
LS refinement shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.28 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.259

+
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