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- PDB-4hw8: 2.25 Angstrom Structure of the Extracellular Solute-binding Prote... -

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Basic information

Entry
Database: PDB / ID: 4hw8
Title2.25 Angstrom Structure of the Extracellular Solute-binding Protein from Staphylococcus aureus in complex with Maltose.
ComponentsBacterial extracellular solute-binding protein, putative
KeywordsSOLUTE-BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / extracellular
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
Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-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 speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.25 Angstrom Structure of the Extracellular Solute-binding Protein from Staphylococcus aureus in complex with Maltose.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial extracellular solute-binding protein, putative
B: Bacterial extracellular solute-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,92425
Polymers95,6322
Non-polymers2,29223
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-166 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.363, 102.363, 190.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Bacterial extracellular solute-binding protein, putative


Mass: 47816.090 Da / Num. of mol.: 2 / Fragment: extracellular solute-binding protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_00176 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2G1E9
#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

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Non-polymers , 4 types, 548 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.4mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (A6), 0.1M Tris-HCl pH 8.5, 2M Ammonium sulfate., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 18, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 53334 / Num. obs: 53334 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.6 / % possible all: 97.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZY0

2zy0


Resolution: 2.251→29.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.629 / SU ML: 0.095
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21499 2699 5.1 %RANDOM
Rwork0.16626 ---
obs0.16872 50571 99.86 %-
all-50571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.478 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å21.43 Å20 Å2
2--2.86 Å20 Å2
3----4.29 Å2
Refinement stepCycle: LAST / Resolution: 2.251→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 123 527 6682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226501
X-RAY DIFFRACTIONr_bond_other_d0.0010.024423
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9778820
X-RAY DIFFRACTIONr_angle_other_deg0.83310920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1625798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5926.146301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.526151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3571510
X-RAY DIFFRACTIONr_chiral_restr0.090.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9591.53891
X-RAY DIFFRACTIONr_mcbond_other0.2551.51567
X-RAY DIFFRACTIONr_mcangle_it1.77826296
X-RAY DIFFRACTIONr_scbond_it2.9833.52610
X-RAY DIFFRACTIONr_scangle_it4.30442524
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.251→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 179 -
Rwork0.258 3667 -
obs--98.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2439-0.1714-0.76742.73441.41163.5770.0091-0.14750.0952-0.27980.2065-0.5032-0.18740.3976-0.21560.11760.0690.03380.1508-0.06230.122284.3911-21.7992-7.5742
21.2966-0.1664-0.41881.73620.95662.7715-0.1071-0.1544-0.02730.0970.08330.13410.1144-0.13470.02380.0334-0.0062-0.00230.1050.01580.01853.634-21.50821.7829
31.36830.17560.42281.62730.86473.0997-0.1539-0.02940.035-0.09470.12910.1028-0.1015-0.12870.02490.03340.00320.00690.09050.00410.028352.2859-15.31571.9946
41.86990.197-0.56591.64690.57521.8884-0.0791-0.30410.09630.06030.1895-0.23610.07620.359-0.11030.05680.0796-0.02540.1605-0.05950.044977.534-20.3953-0.0123
54.314-0.2444-0.95580.5031-0.36383.17440.01820.2743-0.2257-0.1342-0.08910.16530.3981-0.35540.07090.1567-0.0694-0.02270.1526-0.03850.07852.4068-30.7711-15.0699
63.0263-0.2844-0.04122.3961.70723.0003-0.1901-0.09580.34860.08120.3952-0.3087-0.0450.3573-0.20510.1521-0.0193-0.00720.0799-0.06720.087574.14053.8572-25.3225
71.14410.0843-0.72111.83941.06063.3324-0.09510.14870.0325-0.21880.10240.10560.0283-0.3743-0.00730.0508-0.0706-0.02240.15780.02760.010851.9538-17.3098-34.3367
81.58040.0756-1.65351.39090.39723.7506-0.1652-0.0209-0.0669-0.10730.1257-0.03050.3838-0.07970.03950.1078-0.0735-0.01590.1243-0.00780.027355.405-23.3505-34.1079
91.60230.1064-0.07251.4720.7541.8629-0.11660.07090.0866-0.190.2256-0.1877-0.15130.1724-0.1090.127-0.05770.03030.0444-0.02850.031969.5101-2.0584-33.021
103.02941.93050.49544.55161.50283.7436-0.0192-0.03270.0550.2378-0.01540.362-0.1212-0.59410.03460.03940.03810.02390.21210.0280.042344.5879-11.2645-17.6743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 152
2X-RAY DIFFRACTION2A153 - 227
3X-RAY DIFFRACTION3A228 - 298
4X-RAY DIFFRACTION4A299 - 376
5X-RAY DIFFRACTION5A377 - 415
6X-RAY DIFFRACTION6B40 - 152
7X-RAY DIFFRACTION7B153 - 227
8X-RAY DIFFRACTION8B228 - 296
9X-RAY DIFFRACTION9B297 - 376
10X-RAY DIFFRACTION10B377 - 415

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