[English] 日本語
Yorodumi
- PDB-1urg: X-ray structures from the maltose-maltodextrin binding protein of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1urg
TitleX-ray structures from the maltose-maltodextrin binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius
ComponentsMALTOSE-BINDING PROTEIN
KeywordsMALTOSE-BINDING PROTEIN / MALTODEXTRIN-BINDING PROTEIN / ACIDOPHILE / THERMOACIDOPHILE / HYPERTHERMOPHILE / THERMOPHILE
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsSchafer, K. / Magnusson, U. / Scheffel, F. / Schiefner, A. / Sandgren, M.O.J. / Diederichs, K. / Welte, W. / Hulsmann, A. / Schneider, E. / Mowbray, S.L.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: X-Ray Structures of the Maltose-Maltodextrin-Binding Protein of the Thermoacidophilic Bacterium Alicyclobacillus Acidocaldarius Provide Insight Into Acid Stability of Proteins.
Authors: Schafer, K. / Magnusson, U. / Scheffel, F. / Schiefner, A. / Sandgren, M.O.J. / Diederichs, K. / Welte, W. / Hulsmann, A. / Schneider, E. / Mowbray, S.L.
History
DepositionOct 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / struct_conn / 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 / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MALTOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6552
Polymers43,3131
Non-polymers3421
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.110, 72.160, 57.780
Angle α, β, γ (deg.)90.00, 109.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MALTOSE-BINDING PROTEIN


Mass: 43312.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
Plasmid: PFR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: Q9RHZ6
#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.: 171 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growpH: 9.5 / Details: pH 9.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.6 mg/mlprotein1drop
250 mMTris-HCl1droppH7.2
35 %glycerol1drop
410 mMmaltose1drop
520 %(w/v)PEG80001reservoir
6100 mMCHES1reservoirpH9.5

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35989 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / % possible all: 91.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.155
Reflection shell
*PLUS
% possible obs: 91.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
XDSV. 2002data reduction
XSCALEV. 2002data scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1ANF

1anf


Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1722 4.8 %RANDOM
Rwork0.194 ---
obs0.194 34421 95.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.086 Å20 Å2-0.95 Å2
2--1.472 Å20 Å2
3----0.386 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 23 171 3061
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3751.5
X-RAY DIFFRACTIONc_mcangle_it2.1272
X-RAY DIFFRACTIONc_scbond_it2.1622
X-RAY DIFFRACTIONc_scangle_it3.2082.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å
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