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- PDB-5br1: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I... -

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Basic information

Entry
Database: PDB / ID: 5br1
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS S4 (Avi_5305, TARGET EFI-511224) WITH BOUND ALPHA-D-GALACTOSAMINE
ComponentsABC transporter, binding proteinATP-binding cassette transporter
KeywordsSOLUTE-BINDING PROTEIN / Solute binding protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


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
2-amino-2-deoxy-alpha-D-galactopyranose / ABC transporter, binding protein
Similarity search - Component
Biological speciesAgrobacterium vitis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYadava, U. / 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. ...Yadava, U. / 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: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine.
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N. / Carter, M.S. / Gerlt, J.A. / Almo, S.C.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6142
Polymers37,4351
Non-polymers1791
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.781, 63.701, 119.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter, binding protein / ATP-binding cassette transporter


Mass: 37434.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis (bacteria) / Strain: S4 / ATCC BAA-846 / Gene: Avi_5305 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9K0Q5
#2: Sugar ChemComp-X6X / 2-amino-2-deoxy-alpha-D-galactopyranose / alpha-D-galactosamine / 2-amino-2-deoxy-alpha-D-galactose / 2-amino-2-deoxy-D-galactose / 2-amino-2-deoxy-galactose


Type: D-saccharide, alpha linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGalpNaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.87 Å3/Da / Density % sol: 34.26 % / Description: sheet
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (53.5 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-galactosamine); Reservoir (42.1 %(w/v) PEG 4000); Cryoprotection (Reservoir, Pause in air during transfer to liquid N2)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54056 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 21, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.85→16.6 Å / Num. obs: 21553 / % possible obs: 87 % / Redundancy: 4.9 % / Biso Wilson estimate: 21.92 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.059 / Rrim(I) all: 0.141 / Χ2: 0.912 / Net I/av σ(I): 10.136 / Net I/σ(I): 6.8 / Num. measured all: 106215
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.882.80.6087820.5260.3970.7310.81864.8
1.88-1.923.10.5978560.4550.3740.7090.88271
1.92-1.953.40.4939830.6070.2930.5780.87779.2
1.95-1.993.80.44810620.7510.2460.5140.87987.7
1.99-2.045.10.39711210.8150.1850.4410.88991.6
2.04-2.085.30.3410780.8470.1540.3760.98690.4
2.08-2.145.40.29711130.8920.1350.3280.88690.6
2.14-2.195.40.25711010.9240.1170.2840.91890.4
2.19-2.265.40.23911180.9240.1090.2650.95791.2
2.26-2.335.20.21611130.9410.10.240.94691.5
2.33-2.415.20.18411150.9560.0860.2050.89290.8
2.41-2.515.30.16411450.9670.0740.1810.88491.8
2.51-2.625.30.1511380.9730.0680.1650.8992.1
2.62-2.765.40.13311200.9740.060.1470.95590.8
2.76-2.935.30.11311370.9780.0520.1250.88592
2.93-3.165.30.111340.9830.0450.1110.89691.2
3.16-3.475.30.08911160.9860.040.0980.94588.8
3.47-3.975.10.08110820.9860.0370.090.96484.9
3.97-4.985.10.07610620.9870.0350.0840.98982.3
4.98-16.650.06611770.990.030.0730.79485.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IOY

2ioy


Resolution: 1.85→16.499 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2828 1032 4.92 %
Rwork0.1827 19929 -
obs0.1877 20961 84.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 287.38 Å2 / Biso mean: 34.6342 Å2 / Biso min: 9.87 Å2
Refinement stepCycle: final / Resolution: 1.85→16.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 12 249 2642
Biso mean--24.07 31.9 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132447
X-RAY DIFFRACTIONf_angle_d1.3973330
X-RAY DIFFRACTIONf_chiral_restr0.061392
X-RAY DIFFRACTIONf_plane_restr0.008429
X-RAY DIFFRACTIONf_dihedral_angle_d13.543912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8496-1.9470.32191060.28811913201958
1.947-2.06870.34951530.24032858301187
2.0687-2.22810.29951590.20242996315591
2.2281-2.45170.28031590.19163035319491
2.4517-2.80490.30951420.19163092323492
2.8049-3.52820.28581430.1693065320890
3.5282-16.49990.24441700.15272970314084
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)
10.9946-0.09570.01924.7108-2.04664.2486-0.0205-0.2301-0.06450.32020.09710.1434-0.2073-0.0664-0.1090.17120.01540.01870.25780.0080.19-15.8674-3.782824.1361
20.8978-0.7579-0.93060.73260.47942.34890.0614-0.25680.17940.3042-0.1330.0264-0.32470.19210.03240.2883-0.0099-0.03050.2908-0.02050.2053-5.2431-0.562131.0555
30.37360.36760.35342.0832-0.66844.69180.1074-0.2857-0.21480.36070.0558-0.35940.06610.15470.0070.28580.0073-0.05160.3304-0.01610.2445-1.9156-7.655131.6553
40.5009-0.0555-0.22180.8221-0.39291.86840.0615-0.0929-0.04010.0292-0.0021-0.0170.08830.28090.04190.10060.0006-0.01680.1282-0.00720.1772-0.8493-7.1476.9463
50.9319-0.1636-0.06921.05020.21991.12940.0188-0.01410.0213-0.02690.00040.0014-0.0313-0.0532-0.00480.1185-0.0235-0.00530.10570.00110.1372-0.19465.9851.5486
62.91571.4835-0.22915.9287-3.5194.382-0.0440.4705-0.0777-0.14930.04910.15090.05180.11880.09280.13610.013-0.02550.1907-0.03060.1337-12.38413.5212-2.8374
70.6239-0.36350.37512.2868-2.5695.2442-0.03560.04370.03450.0150.17810.18440.2052-0.4693-0.18860.1257-0.03240.00260.14490.01560.1841-12.0659-5.71797.1332
84.8273-2.9197-2.33633.74354.59556.2958-0.0685-0.20840.04390.1903-0.2459-0.14570.3141-0.09820.34150.3242-0.1168-0.00410.35250.08510.2368-9.347-20.417727.2397
92.5459-1.1141.96942.3934-1.78143.29160.0444-0.1203-0.2367-0.10680.07340.09620.2539-0.1048-0.11320.17410.00030.03610.11990.00940.1811-11.7979-15.038311.3919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 68 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 97 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 114 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 150 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 236 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 237 through 260 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 261 through 278 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 279 through 293 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 294 through 346 )A0

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