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- PDB-1urs: X-ray structures of the maltose-maltodextrin binding protein of t... -

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Basic information

Entry
Database: PDB / ID: 1urs
TitleX-ray structures of 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-maltotriose / Maltodextrin-binding protein
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionNov 4, 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.auth_asym_id / _atom_site.auth_atom_id ..._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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTOSE-BINDING PROTEIN
B: MALTOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6344
Polymers86,6252
Non-polymers1,0092
Water9,008500
1
A: MALTOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8172
Polymers43,3131
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MALTOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8172
Polymers43,3131
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.180, 70.530, 104.060
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MALTOSE-BINDING PROTEIN


Mass: 43312.719 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: Q9RHZ6
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growpH: 9.5 / Details: PEG 8000, CHES, PH 9.5, 10% GLYCEROL
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91964
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91964 Å / Relative weight: 1
ReflectionResolution: 1.45→40.14 Å / Num. obs: 137804 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.0084 / Net I/σ(I): 12.7
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 40.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSV. 2002data reduction
XDSV. 2002data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1URG

1urg


Resolution: 1.45→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3450 2.5 %RANDOM
Rwork0.21 ---
obs0.21 137798 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.45→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 68 500 6205
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_deg1.21
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_it1.0891.5
X-RAY DIFFRACTIONc_mcangle_it1.7042
X-RAY DIFFRACTIONc_scbond_it1.9332
X-RAY DIFFRACTIONc_scangle_it2.6572.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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