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- PDB-6h0h: The ABC transporter associated binding protein from B. animalis s... -

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Basic information

Entry
Database: PDB / ID: 6h0h
TitleThe ABC transporter associated binding protein from B. animalis subsp. lactis Bl-04 in complex with beta-1,6-galactobiose
ComponentsProbable solute binding protein of ABC transporter system for sugars
KeywordsSUGAR BINDING PROTEIN / complex / ABC transporter / galactobiose
Function / homologyBacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / transmembrane transport / beta-D-galactopyranose / alpha-D-galactopyranose / DI(HYDROXYETHYL)ETHER / Probable solute binding protein of ABC transporter system for sugars
Function and homology information
Biological speciesBifidobacterium animalis subsp. lactis Bl-04 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsFredslund, F. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research4002-00297 Denmark
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Substrate preference of an ABC importer corresponds to selective growth on beta-(1,6)-galactosides inBifidobacterium animalissubsp.lactis.
Authors: Theilmann, M.C. / Fredslund, F. / Svensson, B. / Lo Leggio, L. / Abou Hachem, M.
History
DepositionJul 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 solute binding protein of ABC transporter system for sugars
B: Probable solute binding protein of ABC transporter system for sugars
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,83412
Polymers92,7402
Non-polymers2,09410
Water22,1761231
1
A: Probable solute binding protein of ABC transporter system for sugars
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3736
Polymers46,3701
Non-polymers1,0035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable solute binding protein of ABC transporter system for sugars
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4616
Polymers46,3701
Non-polymers1,0915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.350, 71.690, 88.710
Angle α, β, γ (deg.)90.00, 95.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable solute binding protein of ABC transporter system for sugars


Mass: 46370.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis Bl-04 (bacteria)
Strain: AD011 / Gene: BLA_0461 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B8DWA9

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-GLA / alpha-D-galactopyranose / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-GAL / beta-D-galactopyranose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1235 molecules

#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1231 / 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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 10 % PEG 1000 10 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→30.211 Å / Num. obs: 130307 / % possible obs: 91.81 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04525 / Rpim(I) all: 0.02629 / Rrim(I) all: 0.05249 / Net I/σ(I): 18.59
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.3927 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 8129 / CC1/2: 0.799 / Rpim(I) all: 0.3028 / Rrim(I) all: 0.499 / % possible all: 57.69

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.39→30.211 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.99
RfactorNum. reflection% reflection
Rfree0.1464 6526 5.03 %
Rwork0.1161 --
obs0.1176 129669 91.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.39→30.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 138 1231 7723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077114
X-RAY DIFFRACTIONf_angle_d0.9279721
X-RAY DIFFRACTIONf_dihedral_angle_d15.5342623
X-RAY DIFFRACTIONf_chiral_restr0.0761035
X-RAY DIFFRACTIONf_plane_restr0.0061273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.40580.23271540.21982410X-RAY DIFFRACTION54
1.4058-1.42230.24541180.20552531X-RAY DIFFRACTION57
1.4223-1.43970.22751550.19672761X-RAY DIFFRACTION62
1.4397-1.45790.2191650.18862951X-RAY DIFFRACTION67
1.4579-1.47710.21711830.18173216X-RAY DIFFRACTION72
1.4771-1.49730.20991870.17723495X-RAY DIFFRACTION78
1.4973-1.51870.20481890.16693888X-RAY DIFFRACTION87
1.5187-1.54140.192220.15954183X-RAY DIFFRACTION95
1.5414-1.56550.1792250.1434426X-RAY DIFFRACTION98
1.5655-1.59110.15432340.13834377X-RAY DIFFRACTION98
1.5911-1.61860.1542370.1344360X-RAY DIFFRACTION99
1.6186-1.6480.16382330.12584386X-RAY DIFFRACTION99
1.648-1.67970.16862300.12514412X-RAY DIFFRACTION99
1.6797-1.7140.1562270.12144430X-RAY DIFFRACTION99
1.714-1.75120.1642530.11574384X-RAY DIFFRACTION99
1.7512-1.7920.14382320.11424426X-RAY DIFFRACTION99
1.792-1.83680.15332390.114421X-RAY DIFFRACTION99
1.8368-1.88640.13671960.11014461X-RAY DIFFRACTION99
1.8864-1.94190.1412440.11244454X-RAY DIFFRACTION99
1.9419-2.00460.14772360.10744412X-RAY DIFFRACTION100
2.0046-2.07620.13912120.10134494X-RAY DIFFRACTION100
2.0762-2.15930.12522300.10014457X-RAY DIFFRACTION100
2.1593-2.25760.12552630.09634416X-RAY DIFFRACTION100
2.2576-2.37660.13772530.09744465X-RAY DIFFRACTION100
2.3766-2.52540.12492320.10124478X-RAY DIFFRACTION100
2.5254-2.72030.12862450.10454435X-RAY DIFFRACTION100
2.7203-2.99380.13752500.10994480X-RAY DIFFRACTION100
2.9938-3.42650.14492160.10724506X-RAY DIFFRACTION99
3.4265-4.3150.12152290.09774491X-RAY DIFFRACTION99
4.315-30.21780.1512370.134537X-RAY DIFFRACTION98
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)
10.4357-0.27510.00770.47250.27190.2965-0.0483-0.0669-0.0640.05780.03450.04610.1101-0.0292-00.1113-0.0024-0.01510.08380.01050.07417.712231.788672.5386
20.03370.0282-0.06810.12660.01080.1419-0.02730.036-0.02880.01930.0426-0.10.00410.104900.0982-0.01010.00510.1102-0.00630.115529.162429.509762.2962
30.4191-0.12440.37870.50830.17960.81180.0053-0.0628-0.05480.0297-0.0074-0.03540.12780.00730.00020.11840.0025-0.01520.0952-0.00060.085121.924625.927480.1465
40.47280.0257-0.11020.2408-0.13210.42680.00680.01070.06590.00750.01610.0367-0.0055-0.0627-00.1032-0.0074-0.00570.0854-0.00060.09738.638136.534568.9367
50.1354-0.02290.16340.28930.00930.2277-0.0942-0.0351-0.07150.06810.04190.01870.2323-0.059800.1451-0.0073-0.01350.10970.00690.094819.87824.995495.338
60.1870.11410.1390.2817-0.05810.2185-0.0440.0785-0.1315-0.0974-0.0256-0.0110.2034-0.014100.1328-0.00010.02310.1038-0.01740.138315.479453.362445.4284
70.6365-0.16970.24430.57550.20930.3406-0.0196-0.0214-0.02530.0244-0.0113-0.12720.01290.109700.0726-0.0014-0.00040.08380.00240.106621.57365.300354.2981
80.1875-0.33570.02370.6515-0.09690.74560.0267-0.02110.057-0.01670.0071-0.0133-0.0368-0.033-00.0656-0.0029-0.01280.0714-0.00720.06116.871472.29552.261
90.24570.01820.24480.896-0.18840.9803-0.009-0.03020.05140.06330.03720.1269-0.0617-0.18330.00040.08810.02530.01530.1076-0.00030.091-2.540175.915264.2146
100.08190.08330.1550.3851-0.03540.3664-0.00710.00180.10150.07030.00660.0382-0.0999-0.03900.13450.00050.01530.1103-0.00580.09917.757380.761370.7421
110.6308-0.1504-0.08360.3173-0.12810.6231-0.01140.0569-0.0364-0.00320.00530.02980.0138-0.1153-00.0718-0.0099-0.00340.0827-0.00180.093.074767.800450.2419
120.3753-0.33740.27640.7524-0.02630.490.0373-0.1205-0.01790.0935-0.0485-0.0379-0.0719-0.005700.1365-0.006-0.00860.1110.00150.093814.543873.12274.5877
130.37230.1609-0.0160.516-0.01940.277-0.0262-0.12070.36370.14490.05940.0436-0.1584-0.09280.00320.11150.01620.00770.101-0.00290.13070.096947.880582.4067
140.2691-0.1047-0.17360.2486-0.09410.2131-0.0364-0.0798-0.03960.05720.04150.08910.173-0.148200.1455-0.02330.00490.15150.01820.1157-2.847932.633384.2622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 107 through 140 )
2X-RAY DIFFRACTION2chain 'B' and (resid 141 through 164 )
3X-RAY DIFFRACTION3chain 'B' and (resid 165 through 223 )
4X-RAY DIFFRACTION4chain 'B' and (resid 224 through 381 )
5X-RAY DIFFRACTION5chain 'B' and (resid 403 through 427 )
6X-RAY DIFFRACTION6chain 'A' and (resid 18 through 53 )
7X-RAY DIFFRACTION7chain 'A' and (resid 54 through 106 )
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 141 )
9X-RAY DIFFRACTION9chain 'A' and (resid 142 through 198 )
10X-RAY DIFFRACTION10chain 'A' and (resid 199 through 223 )
11X-RAY DIFFRACTION11chain 'A' and (resid 224 through 381 )
12X-RAY DIFFRACTION12chain 'A' and (resid 382 through 427 )
13X-RAY DIFFRACTION13chain 'B' and (resid 18 through 73 )
14X-RAY DIFFRACTION14chain 'B' and (resid 74 through 106 )

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