[English] 日本語
Yorodumi
- PDB-1mdp: REFINED STRUCTURES OF TWO INSERTION(SLASH)DELETION MUTANTS PROBE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mdp
TitleREFINED STRUCTURES OF TWO INSERTION(SLASH)DELETION MUTANTS PROBE FUNCTION OF THE MALTODEXTRIN BINDING PROTEIN
ComponentsMALTODEXTRIN BINDING PROTEIN
KeywordsSUGAR TRANSPORT
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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 / Resolution: 2.3 Å
AuthorsSharff, A.J. / Quiocho, F.A.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Refined structures of two insertion/deletion mutants probe function of the maltodextrin binding protein.
Authors: Sharff, A.J. / Rodseth, L.E. / Szmelcman, S. / Hofnung, M. / Quiocho, F.A.
#1: 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 Transport and Chemotaxis
Authors: Sharff, A.J. / Rodseth, L.E. / Spurlino, J.C. / Quiocho, F.A.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: The 2.3 Angstroms 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.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Silent and Functional Changes in the Periplasmic Maltose-Binding Protein of Escherichia Coli K12 II. Chemotaxis Towards Maltose
Authors: Duplay, P. / Szmelcman, S.
#4: Journal: J.Mol.Biol. / Year: 1987
Title: Silent and Functional Changes in the Periplasmic Maltose-Binding Protein of Escherichia Coli K12 I. Transport of Maltose
Authors: Duplay, P. / Szmelcman, S. / Bedouelle, H. / Hofnung, M.
History
DepositionAug 10, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: MALTODEXTRIN BINDING PROTEIN
2: MALTODEXTRIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6154
Polymers79,9302
Non-polymers6852
Water2,900161
1
1: MALTODEXTRIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3072
Polymers39,9651
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
2: MALTODEXTRIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3072
Polymers39,9651
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.510, 88.330, 75.790
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.1615, -0.652099, -0.740699), (-0.649799, -0.635199, 0.4175), (-0.742799, 0.4139, -0.526299)
Vector: 101.6252, 92.0499, 78.0878)

-
Components

#1: Protein MALTODEXTRIN BINDING PROTEIN


Mass: 39965.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Details: microseeding into drops of 18-20 % PEG over 18-25 % PEG
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
22-3 mMmaltose1drop
310-12.5 %PEG60001drop
410 mMsodium citrate1drop
50.02 %sodium azide1drop
614-16 %PEG1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 39720 / % possible obs: 74 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. measured all: 62502 / Rmerge(I) obs: 0.0421

-
Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.187 -
obs0.187 9957
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5644 0 46 161 5851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.025
X-RAY DIFFRACTIONp_dihedral_angle_d0.050.03
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.020.009
X-RAY DIFFRACTIONp_chiral_restr0.150.107
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

+
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