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- PDB-2w7y: Structure of a Streptococcus pneumoniae solute-binding protein in... -

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Entry
Database: PDB / ID: 2w7y
TitleStructure of a Streptococcus pneumoniae solute-binding protein in complex with the blood group A-trisaccharide.
ComponentsPROBABLE SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / SOLUTE-BINDING PROTEIN / STREPTOCOCCUS PNEUMONIAE / BLOOD GROUP ANTIGEN / CARBOHYDRATE TRANSPORT
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / IODIDE ION / :
Function and homology information
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsHiggins, M.A. / Abbott, D.W. / Boulanger, M.J. / Boraston, A.B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Blood-Group Antigen Recognition by a Solute-Binding Protein from a Serotype 3 Strain of Streptococcus Pneumoniae.
Authors: Higgins, M.A. / Abbott, D.W. / Boulanger, M.J. / Boraston, A.B.
History
DepositionJan 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: 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 / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN
B: PROBABLE SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6536
Polymers94,3402
Non-polymers1,3134
Water7,386410
1
A: PROBABLE SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8263
Polymers47,1701
Non-polymers6562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROBABLE SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8263
Polymers47,1701
Non-polymers6562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.990, 104.900, 97.700
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A38 - 383
2111B38 - 383

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Components

#1: Protein PROBABLE SUGAR ABC TRANSPORTER, SUGAR-BINDING PROTEIN / FCSSBP


Mass: 47169.984 Da / Num. of mol.: 2 / Fragment: SOLUTE-BINDING PROTEIN, RESIDUES 24-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: SP3-BS71 / Plasmid: PSBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5LBQ6
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.94 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97884
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97884 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 31126 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.35→97.59 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.293 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.671 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26311 1569 5 %RANDOM
Rwork0.21339 ---
obs0.21592 29535 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.21 Å2
2--1.71 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.35→97.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 74 410 6450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9648316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68726.567268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.402151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.744158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.23150
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.24198
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.181.53870
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.17826178
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.45532482
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5764.52138
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2983 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.03 Å

Dom-IDAuth asym-IDTypeWeight position
1Atight positional0.05
2Btight positional0.05
1Atight thermal0.5
2Btight thermal0.5
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 103
Rwork0.257 2180
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)
13.2695-0.7665-0.38245.7694-2.111.5591-0.263-0.43860.16760.29870.2123-0.328-0.08620.14310.0507-0.1170.0181-0.0580.0828-0.0628-0.041725.48854.601363.8667
25.0822-1.0571-0.02342.4489-0.28382.2767-0.3608-0.5971-0.44550.21070.35670.27560.1537-0.41590.0042-0.05570.05330.0420.07870.0665-0.122712.2872-5.173965.4454
30.59460.08030.48880.3289-0.01882.3725-0.07950.12120.0193-0.16270.03720.02140.08510.04570.0423-0.0687-0.01640.0032-0.0274-0.0065-0.04495.83661.360636.4362
46.85380.4631-0.27045.2741-0.29451.2846-0.09940.6450.3221-0.26880.0859-0.21260.12560.35150.0136-0.0429-0.0035-0.0432-0.0639-0.0133-0.068912.8935-2.375333.5977
55.3145-0.10020.96582.6632-2.049111.02980.00780.0314-0.4276-0.03580.06560.50510.7912-0.5711-0.07350.0127-0.07230.0447-0.1346-0.02630.09585.8245-18.652943.7875
63.4495-2.057-2.38059.81992.3948.3673-0.05190.0238-0.1462-0.36370.2916-0.8744-0.26650.3884-0.2397-0.17410.00640.02660.077-0.0645-0.060717.5897-4.115932.4801
71.4674-0.33020.36711.40820.5872.5729-0.0648-0.23820.19010.0330.046-0.0007-0.23670.07120.0188-0.12440.00480.0036-0.056-0.0128-0.07111.45116.759653.4685
82.4272-1.1355-0.67442.82860.82432.2429-0.07810.0242-0.03670.04130.04740.1963-0.0511-0.0990.0307-0.163-0.02960.0257-0.0860.0028-0.10997.76270.874445.8696
93.7354-0.46470.57225.3106-1.59262.0067-0.04930.19770.09010.21930.025-0.5544-0.0350.09830.0242-0.0018-0.0758-0.03120.0424-0.0129-0.00946.2663-23.078482.1982
104.4407-1.24831.70592.8998-0.93573.8729-0.29120.18380.38850.12040.1318-0.0313-0.2468-0.67090.1594-0.0144-0.0429-0.04790.09930.0191-0.130631.7076-17.294878.9121
110.7140.2657-0.87210.1304-0.04933.4689-0.15170.0433-0.0350.1377-0.005-0.0405-0.1012-0.07090.15670.0140.0163-0.00190.00830.0045-0.048424.0689-23.6907106.0728
126.08760.8561-0.73014.25240.71443.9193-0.3377-0.13310.16810.06810.11630.1274-0.22860.05870.2214-0.0292-0.003-0.041-0.1023-0.046-0.058328.649-18.3944109.8873
132.67410.07861.9016.5365-1.63825.6076-0.31240.04850.5178-0.34050.11970.0789-0.44060.01870.19260.0766-0.0401-0.0416-0.04290.00130.036230.7737-11.9816105.9765
140.32040.3129-0.54540.3424-0.86333.8964-0.29020.1201-0.550.22380.2031-0.19950.61260.1430.0870.12060.0163-0.0008-0.07570.02730.01329.5347-32.5034105.6883
151.9732-0.1095-1.32161.30610.10523.0196-0.28060.4916-0.3817-0.07980.0470.04390.2385-0.46180.2336-0.0556-0.1029-0.01530.1671-0.0399-0.048527.4525-29.813884.0695
163.88212.57941.41662.98941.7092.1264-0.4002-0.01370.3825-0.29010.15230.0925-0.4279-0.0690.24790.0660.0263-0.0899-0.09410.029-0.019531.0029-13.4185102.5715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 55
2X-RAY DIFFRACTION2A56 - 103
3X-RAY DIFFRACTION3A104 - 148
4X-RAY DIFFRACTION4A149 - 169
5X-RAY DIFFRACTION5A170 - 199
6X-RAY DIFFRACTION6A200 - 221
7X-RAY DIFFRACTION7A222 - 310
8X-RAY DIFFRACTION8A311 - 365
9X-RAY DIFFRACTION9B38 - 52
10X-RAY DIFFRACTION10B53 - 101
11X-RAY DIFFRACTION11B102 - 146
12X-RAY DIFFRACTION12B147 - 175
13X-RAY DIFFRACTION13B176 - 224
14X-RAY DIFFRACTION14B225 - 252
15X-RAY DIFFRACTION15B253 - 322
16X-RAY DIFFRACTION16B323 - 383

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