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- PDB-4hs7: 2.6 Angstrom Structure of the Extracellular Solute-binding Protei... -

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Basic information

Entry
Database: PDB / ID: 4hs7
Title2.6 Angstrom Structure of the Extracellular Solute-binding Protein from Staphylococcus aureus in complex with PEG.
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
: / DI(HYDROXYETHYL)ETHER / Maltodextrin-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: 2.6 Angstrom Structure of the Extracellular Solute-binding Protein from Staphylococcus aureus in complex with PEG.
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
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)96,5758
Polymers95,6322
Non-polymers9436
Water5,242291
1
A: Bacterial extracellular solute-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2884
Polymers47,8161
Non-polymers4723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bacterial extracellular solute-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2884
Polymers47,8161
Non-polymers4723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.863, 101.863, 191.341
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.4mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: JCSG+ (B12), 0.2M tri-Potassium citrate pH 8.3, 20% (w/v) PEG 3350, 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: 2.6→30 Å / Num. all: 34117 / Num. obs: 34117 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 3 / Num. unique all: 1701 / % possible all: 99.6

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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 2ZYO

2zyo


Resolution: 2.6→29.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 19.355 / SU ML: 0.186
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21933 1721 5 %RANDOM
Rwork0.16742 ---
all0.17003 32393 --
obs0.17003 32393 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.585 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å21.52 Å20 Å2
2--3.05 Å20 Å2
3----4.57 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 60 291 6383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226394
X-RAY DIFFRACTIONr_bond_other_d0.0010.024434
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9658631
X-RAY DIFFRACTIONr_angle_other_deg0.805310929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8855788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75626.02294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.515151175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9491510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021196
X-RAY DIFFRACTIONr_mcbond_it1.0441.53856
X-RAY DIFFRACTIONr_mcbond_other0.2461.51556
X-RAY DIFFRACTIONr_mcangle_it1.97926233
X-RAY DIFFRACTIONr_scbond_it3.39332538
X-RAY DIFFRACTIONr_scangle_it5.3584.52398
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 121 -
Rwork0.229 2377 -
obs-2377 99.56 %
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)
12.9753-0.7441-0.02523.3114-1.10413.30070.05820.17150.01530.441-0.00870.4248-0.2356-0.072-0.04960.1164-0.06430.08710.1666-0.01160.097410.3783-26.22226.8476
21.97740.7697-0.97421.9837-0.96593.74020.00130.2172-0.0836-0.14570.0632-0.10770.2831-0.0014-0.06450.09070.0791-0.01230.1131-0.03350.036440.0367-35.2167-2.4119
31.7513-0.28130.44792.0658-1.37063.5581-0.05420.1925-0.02750.05840.0804-0.06790.0660.1168-0.02620.07850.04110.05980.1638-0.00490.069343.2051-29.4841-2.4599
42.402-0.12-0.80222.1888-0.38141.22620.04310.47660.12150.0508-0.03910.1306-0.028-0.1543-0.0040.0118-0.01640.00370.15630.02710.019417.5442-27.196-0.5658
55.8728-0.6581-1.45963.0743-0.25365.92120.0868-0.3556-0.58460.1255-0.2062-0.03990.71930.44940.11940.19990.0451-0.00160.11280.00160.104238.2858-44.42414.5573
64.3448-0.3462-1.08562.1038-0.40763.7318-0.12140.39370.4490.10190.1830.1787-0.0889-0.2801-0.06160.2056-0.0570.00970.08390.06890.144427.7249-4.758624.5952
72.47150.4768-1.25332.3827-1.61913.56440.1305-0.0629-0.12780.1791-0.1024-0.0970.00290.2294-0.02810.03860.0085-0.02170.0372-0.01640.028642.8382-31.608434.1806
81.73590.0341-0.76581.360.10993.19270.0190.1454-0.25160.07280.00760.03550.10330.0786-0.02670.08870.02920.0020.04710.00050.077437.5835-36.42833.8795
92.0996-0.2910.04292.2444-0.91221.854-0.14450.00730.10170.30740.12410.105-0.2569-0.08370.02040.1783-0.00580.02760.01290.00040.019830.6128-11.882432.4616
103.2516-2.42651.4517.8008-3.54385.8581-0.02340.2511-0.1249-0.2415-0.1898-0.4891-0.01360.60070.21320.06980.0370.02520.1687-0.01650.06451.5652-28.063317.2269
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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