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- PDB-3jyr: Crystal structures of the GacH receptor of Streptomyces glaucesce... -

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Basic information

Entry
Database: PDB / ID: 3jyr
TitleCrystal structures of the GacH receptor of Streptomyces glaucescens GLA.O in the unliganded form and in complex with acarbose and an acarbose homolog. Comparison with acarbose-loaded maltose binding protein of Salmonella typhimurium.
ComponentsMaltose-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / acarbose / ABC transporter / maltose/maltodextrin-binding protein / Salmonella typhimurium / Periplasm / Sugar transport / Transport
Function / homology
Function and homology information


maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
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-acarbose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsVahedi-Faridi, A. / Licht, A. / Bulut, H. / Schneider, E.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of the Solute Receptor GacH of Streptomyces glaucescens in Complex with Acarbose and an Acarbose Homolog: Comparison with the Acarbose-Loaded Maltose-Binding Protein of Salmonella typhimurium.
Authors: Vahedi-Faridi, A. / Licht, A. / Bulut, H. / Scheffel, F. / Keller, S. / Wehmeier, U.F. / Saenger, W. / Schneider, E.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _atom_site.type_symbol / _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.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8742
Polymers43,2281
Non-polymers6461
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.921, 89.229, 64.163
Angle α, β, γ (deg.)90.00, 112.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

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Components

#1: Protein Maltose-binding periplasmic protein / MMBP / Maltodextrin-binding protein


Mass: 43228.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: malE, STM4229 / Plasmid: pES35 / Production host: Escherichia coli (E. coli) / References: UniProt: P19576
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 18% PEG 8000, 10 mM CITRATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.75→59.13 Å / Num. obs: 37653 / % possible obs: 93.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Χ2: 1.274 / Net I/σ(I): 22.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.812.30.1225750.99864.6
1.81-1.892.50.09531781.05578.6
1.89-1.972.90.0836541.18691.2
1.97-2.073.50.06739881.28499.1
2.07-2.23.90.05240191.213100
2.2-2.383.90.04240321.214100
2.38-2.6140.03740071.235100
2.61-2.9940.03440291.312100
2.99-3.7740.03940771.487100
3.77-403.90.04140941.38999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.12 Å19.71 Å
Translation2.12 Å19.71 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.877 / SU B: 1.957 / SU ML: 0.065 / SU R Cruickshank DPI: 0.118 / SU Rfree: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1889 5 %RANDOM
Rwork0.167 ---
obs0.169 37652 93.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.93 Å2 / Biso mean: 14.635 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.55 Å2
2---0.9 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 44 426 3352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222998
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9794075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3125373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1425.781128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80515504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.361157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022250
X-RAY DIFFRACTIONr_nbd_refined0.1940.21477
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2343
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.225
X-RAY DIFFRACTIONr_mcbond_it0.7511.51907
X-RAY DIFFRACTIONr_mcangle_it1.12922966
X-RAY DIFFRACTIONr_scbond_it2.01131270
X-RAY DIFFRACTIONr_scangle_it3.2354.51107
LS refinement shellResolution: 1.75→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 81 -
Rwork0.187 1723 -
all-1804 -
obs--60.48 %

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