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- PDB-4y9t: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (I... -

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Basic information

Entry
Database: PDB / ID: 4y9t
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS S4 (Avi_5305, TARGET EFI-511224) WITH BOUND ALPHA-D-GLUCOSAMINE
ComponentsABC transporter, solute binding proteinATP-binding cassette transporter
KeywordsSOLUTE-BINDING PROTEIN / ABC TRANSPORTER 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-glucopyranose / ABC transporter, binding protein
Similarity search - Component
Biological speciesAgrobacterium vitis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, 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)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
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
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6142
Polymers37,4351
Non-polymers1791
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.634, 63.611, 127.394
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, solute 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-PA1 / 2-amino-2-deoxy-alpha-D-glucopyranose / Glucosamine


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


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.98 Å3/Da / Density % sol: 37.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (40.65 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-glucosamine); Reservoir (35 %(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: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 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: 1.8→100 Å / Num. obs: 25086 / % possible obs: 88.2 % / Redundancy: 13.3 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.038 / Rrim(I) all: 0.141 / Χ2: 0.972 / Net I/av σ(I): 19.877 / Net I/σ(I): 7.2 / Num. measured all: 333857
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8313.60.7412370.8990.2030.7680.84887.1
1.83-1.8613.80.66212300.9040.1820.6870.86789.8
1.86-1.913.60.56712360.9260.1560.5890.90388.9
1.9-1.9413.70.47212180.9460.130.490.91286.8
1.94-1.9813.60.40812490.9610.1120.4240.94889.2
1.98-2.0313.70.35211980.9740.0970.3650.95286.1
2.03-2.0813.70.28912140.9760.080.30.97188.1
2.08-2.1313.60.25412140.9830.070.2640.96685.6
2.13-2.213.60.23312090.9840.0640.2410.96586.4
2.2-2.2713.60.2112020.9860.0580.2180.95985
2.27-2.3513.40.18212090.9880.0510.1890.93886.5
2.35-2.4413.40.16211960.9920.0450.1680.94283.4
2.44-2.5513.30.15111920.9910.0420.1560.89285.9
2.55-2.6913.20.13112030.9940.0360.1360.88984.7
2.69-2.8613.10.11312100.9950.0320.1180.85184.2
2.86-3.08130.10612110.9940.030.110.8684.7
3.08-3.3912.50.09812620.9930.0280.1020.89488.1
3.39-3.88120.09613720.9890.0280.10.99694.5
3.88-4.8912.70.10214730.9940.0290.1071.17899.4
4.89-10013.20.12415510.9930.0350.1291.52997.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
HKL-3000data reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.801→24.035 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1892 1267 5.08 %
Rwork0.1478 23688 -
obs0.1499 24955 87.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 307.21 Å2 / Biso mean: 26.2422 Å2 / Biso min: 6.19 Å2
Refinement stepCycle: final / Resolution: 1.801→24.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 12 319 2708
Biso mean--11.15 29.08 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112436
X-RAY DIFFRACTIONf_angle_d1.3213318
X-RAY DIFFRACTIONf_chiral_restr0.08393
X-RAY DIFFRACTIONf_plane_restr0.008428
X-RAY DIFFRACTIONf_dihedral_angle_d12.826878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8011-1.87320.2591370.192565270287
1.8732-1.95840.22591390.16892576271588
1.9584-2.06160.20161190.1522574269387
2.0616-2.19070.21541480.14862546269486
2.1907-2.35970.22071150.14692532264785
2.3597-2.59690.20221430.15752511265484
2.5969-2.97210.22351250.15632535266084
2.9721-3.74230.19621470.15322720286789
3.7423-24.03750.14211940.12743129332399
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)
10.92360.6309-0.09442.1862-0.31672.2479-0.0690.3764-0.002-0.53510.11180.02150.1444-0.1567-0.01240.2097-0.0025-0.00720.22290.00880.118928.21464.181336.6808
21.24520.33470.05451.4728-0.25921.53260.0341-0.0456-0.05540.0768-0.0417-0.07760.03860.07520.00320.06930.01250.00780.0690.00690.107936.9547-3.539963.1325
31.0314-0.43920.00022.9266-2.2293.08640.0206-0.050.0360.24290.08150.1611-0.1668-0.0897-0.08070.0733-0.00010.0090.089-0.00940.121225.1478-1.608665.503
41.8317-0.33430.37421.81710.08822.65460.06070.40070.3156-0.2757-0.02080.2181-0.6012-0.0668-0.10080.28460.0158-0.01570.2280.07320.203626.345617.578839.8336
52.167-0.0936-0.71711.9138-0.36582.90290.09890.12230.26650.0567-0.1133-0.0713-0.67130.0652-0.00610.1675-0.0044-0.00930.10150.0060.13430.774116.178451.7448
60.61320.6657-0.33821.3275-1.7013.14120.03840.31340.41390.04910.11540.2016-0.6867-0.6611-0.25760.2440.09510.02320.21750.0910.297817.037213.451552.5077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 130 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 236 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 270 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 293 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 325 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 326 through 346 )A0

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