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- PDB-4wut: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I... -

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Database: PDB / ID: 4wut
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS (Avi_5133, TARGET EFI-511220) WITH BOUND D-FUCOSE
ComponentsABC transporter substrate binding protein (Ribose)
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-fucopyranose / ABC transporter substrate binding protein (Ribose)
Similarity search - Component
Biological speciesAgrobacterium vitis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS (Avi_5133, TARGET EFI-511220) WITH BOUND D-FUCOSE
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate binding protein (Ribose)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2057
Polymers33,8541
Non-polymers3516
Water6,630368
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.188, 69.367, 92.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer

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Components

#1: Protein ABC transporter substrate binding protein (Ribose)


Mass: 33854.102 Da / Num. of mol.: 1 / Fragment: ABC TRANSPORTER SOLUTE BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis (bacteria) / Strain: S4 / ATCC BAA-846 / Gene: rbsB, Avi_5133 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9K0B2
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-FCB / beta-D-fucopyranose / beta-D-fucose / 6-deoxy-beta-D-galactopyranose / D-fucose / fucose / Fucose


Type: D-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
DFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fucopyranoseCOMMON NAMEGMML 1.0
b-D-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein (29.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Fucose); Reservoir (0.2 M Calcium Acetate 0.1 M MES pH 6.0, 20 %(w/v) PEG 8000 ); Cryoprotection (80% (50%) Peg 3350, 20% Reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 25, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→42.73 Å / Num. obs: 50200 / % possible obs: 99.6 % / Redundancy: 12.1 % / Biso Wilson estimate: 17.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.027 / Net I/σ(I): 16.1 / Num. measured all: 606632 / Scaling rejects: 1353
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.5-1.5312.10.75732975924610.9260.222100
8.22-42.737.10.08322.916072260.9930.02958.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.1.27data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→26.929 Å / FOM work R set: 0.7636 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 2550 5.09 %
Rwork0.1842 47555 -
obs0.1854 50105 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.92 Å2 / Biso mean: 19.09 Å2 / Biso min: 6.33 Å2
Refinement stepCycle: final / Resolution: 1.5→26.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 16 368 2543
Biso mean--13.83 29.56 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112228
X-RAY DIFFRACTIONf_angle_d1.2623035
X-RAY DIFFRACTIONf_chiral_restr0.076355
X-RAY DIFFRACTIONf_plane_restr0.006387
X-RAY DIFFRACTIONf_dihedral_angle_d13.92830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52890.63021290.67826422771100
1.5289-1.56010.42821640.507925992763100
1.5601-1.5940.49061570.429125892746100
1.594-1.6310.37831360.370726122748100
1.631-1.67180.3591400.322826302770100
1.6718-1.7170.34871200.293126502770100
1.717-1.76750.30871440.265826252769100
1.7675-1.82460.20441460.207926062752100
1.8246-1.88980.18921410.180326452786100
1.8898-1.96540.19531400.177426322772100
1.9654-2.05480.20011400.172726582798100
2.0548-2.16310.14761480.15126422790100
2.1631-2.29860.17961460.144926462792100
2.2986-2.4760.17371070.147626992806100
2.476-2.72490.17611340.149826912825100
2.7249-3.11870.17641520.161926752827100
3.1187-3.92730.18521610.148627042865100
3.9273-26.93340.1821450.16622610275592
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)
10.7556-0.1564-0.77262.64910.38841.4133-0.00430.08660.6116-0.0134-0.0343-0.321-0.26340.08050.06250.13-0.0018-0.02160.10980.07230.252110.426642.61840.929
20.6135-1.15860.0982.3026-0.4110.9287-0.01160.01340.44370.1165-0.02230.0329-0.35080.04740.03240.2021-0.0019-0.02610.11640.03930.3437.822343.936945.9895
31.2086-0.0007-0.11921.9972-0.0341.7295-0.0231-0.05330.23710.17070.04960.0706-0.2431-0.1622-0.01380.11260.0384-0.00490.10110.00050.121-1.973438.198549.4432
42.4239-1.9436-1.5752.18990.58063.0995-0.06040.1562-0.4708-0.1204-0.10610.44820.1915-0.54480.08590.1014-0.0006-0.03290.21340.02180.1964-5.056332.871438.6794
51.2198-0.7614-0.40642.14191.09872.74190.02880.2715-0.1182-0.1071-0.04370.08610.11080.01260.00620.1125-0.0282-0.01160.1734-0.00240.110610.558617.485727.7343
60.6813-0.8025-0.35022.81332.98444.6489-0.03430.2428-0.19930.0482-0.20510.27730.1628-0.41260.17240.0891-0.0193-0.00340.1456-0.02370.09154.439817.942229.9031
71.1247-0.4790.12390.2504-0.29231.2968-0.07360.04730.02120.07550.0560.02470.0620.04150.02820.10.00210.0010.07970.00690.089817.374315.524738.1822
81.1976-0.9619-0.21911.8641-0.09181.06070.09510.28520.2094-0.1218-0.0851-0.3018-0.01740.0661-0.0010.08540.00220.01510.11910.03320.121521.260522.660830.2771
93.1511-1.3657-1.29671.27260.76681.690.04530.28430.254-0.2462-0.133-0.08-0.084-0.16370.0350.2090.0509-0.01380.17270.09810.23651.716745.919935.0284
103.2058-1.4069-0.81941.93930.69290.3969-0.00690.01270.1056-0.1588-0.05820.1825-0.1898-0.00780.04420.20160.0599-0.0080.25150.08870.1538-1.458739.328529.6858
110.352-0.0431-0.85081.25280.10712.07270.190.28510.0894-0.315-0.0727-0.1008-0.1156-0.16070.06030.22530.0710.09760.2480.17860.207617.916835.259121.5186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 51 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 67 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 113 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 132 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 163 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 180 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 181 through 208 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 209 through 266 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 267 through 283 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 284 through 298 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 299 through 313 )A0

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