[English] 日本語
Yorodumi
- PDB-1anf: MALTODEXTRIN BINDING PROTEIN WITH BOUND MALTOSE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1anf
TitleMALTODEXTRIN BINDING PROTEIN WITH BOUND MALTOSE
ComponentsMALTODEXTRIN-BINDING PROTEIN
KeywordsPERIPLASMIC BINDING PROTEIN / SUGAR TRANSPORT
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH 2MBP / Resolution: 1.67 Å
AuthorsSpurlino, J.C. / Quiocho, F.A.
Citation
Journal: Structure / Year: 1997
Title: Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor.
Authors: Quiocho, F.A. / Spurlino, J.C. / Rodseth, L.E.
#1: Journal: Biochemistry / Year: 1993
Title: Refined 1.8-A Structure Reveals the Mode of Binding of Beta-Cyclodextrin to the Maltodextrin Binding Protein
Authors: Sharff, A.J. / Rodseth, L.E. / Quiocho, F.A.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Atomic Interactions in Protein-Carbohydrate Complexes. Tryptophan Residues in the Periplasmic Maltodextrin Receptor for Active Transport and Chemotaxis
Authors: Spurlino, J.C. / Rodseth, L.E. / Quiocho, F.A.
#3: Journal: Biochemistry / Year: 1992
Title: Crystallographic Evidence of a Large Ligand-Induced Hinge-Twist Motion between the Two Domains of the Maltodextrin Binding Protein Involved in Active Transport and Chemotaxis
Authors: Sharff, A.J. / Rodseth, L.E. / Spurlino, J.C. / Quiocho, F.A.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: The 2.3-A Resolution Structure of the Maltose-or Maltodextrin-Binding Protein, a Primary Receptor of Bacterial Active Transport and Chemotaxis
Authors: Spurlino, J.C. / Lu, G.Y. / Quiocho, F.A.
History
DepositionJun 25, 1997Processing site: BNL
SupersessionDec 24, 1997ID: 2MBP
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MALTODEXTRIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0952
Polymers40,7531
Non-polymers3421
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.880, 68.440, 57.940
Angle α, β, γ (deg.)90.00, 112.54, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MALTODEXTRIN-BINDING PROTEIN


Mass: 40753.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: PERIPLASM / Gene: MALE / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.77 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.2
Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 10 MM CITRATE, PH 6.2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlMBP1drop
21 mMmaltodextrin1drop
316 %(w/v)PEG60001drop
422 %(w/v)PEG60001reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 1, 1989 / Details: NA
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→10 Å / Num. obs: 39297 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.0969 / Net I/σ(I): 13.88
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.244 / % possible all: 68
Reflection shell
*PLUS
% possible obs: 68 %

-
Processing

Software
NameVersionClassification
PROTEINmodel building
CHAINmodel building
PROLSQrefinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
SDMSDETECTOR SYSTEM (NIELSEN)data scaling
PROTEINphasing
CHAINphasing
RefinementMethod to determine structure: ISOMORPHOUS WITH 2MBP
Starting model: PDB ENTRY 2MBP

2mbp
PDB Unreleased entry


Resolution: 1.67→10 Å / σ(F): 2 / Details: X-PLOR ALSO WAS USED.
RfactorNum. reflection% reflection
Rwork0.182 --
obs-34825 80 %
Displacement parametersBiso mean: 30.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.67→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 23 104 2987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.02
X-RAY DIFFRACTIONp_angle_d0.0550.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0780.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.541
X-RAY DIFFRACTIONp_mcangle_it2.471.5
X-RAY DIFFRACTIONp_scbond_it3.212
X-RAY DIFFRACTIONp_scangle_it4.752.5
X-RAY DIFFRACTIONp_plane_restr0.0140.015
X-RAY DIFFRACTIONp_chiral_restr0.160.1
X-RAY DIFFRACTIONp_singtor_nbd0.2070.5
X-RAY DIFFRACTIONp_multtor_nbd0.2520.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2240.5
X-RAY DIFFRACTIONp_planar_tor3.53
X-RAY DIFFRACTIONp_staggered_tor21.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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