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- PDB-4wt7: Crystal structure of an ABC transporter solute binding protein (I... -

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Basic information

Entry
Database: PDB / ID: 4wt7
TitleCrystal structure of an ABC transporter solute binding protein (IPR025997) from Agrobacterium vitis (Avi_5165, Target EFI-511223) with bound allitol
ComponentsABC transporter substrate binding protein (Ribose)
KeywordsTRANSPORT PROTEIN / Enzyme Function Initiative / EFI / Structural Genomics
Function / homology
Function and homology information


Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-allitol / ABC transporter substrate binding protein (Ribose)
Similarity search - Component
Biological speciesAgrobacterium vitis S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_5165, Target EFI-511223) with bound allitol
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.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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 substrate binding protein (Ribose)
B: ABC transporter substrate binding protein (Ribose)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3895
Polymers68,9902
Non-polymers4003
Water8,647480
1
A: ABC transporter substrate binding protein (Ribose)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7123
Polymers34,4951
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter substrate binding protein (Ribose)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6772
Polymers34,4951
Non-polymers1821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.080, 83.930, 189.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

Detailsbiological unit is a monomer

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Components

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


Mass: 34494.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis S4 (bacteria) / Gene: rbsB, Avi_5165 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9K0E0
#2: Chemical ChemComp-X9X / D-allitol


Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein (29.0 mg/mL, 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM allitol), reservoir (0.2 M lithium chloride, 20% w/v PEG3350), cryoprotection (80% reservoir + 20% glycerol)

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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 15, 2014 / Details: MIRRORS
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→25.88 Å / Num. obs: 38991 / % possible obs: 93.1 % / Redundancy: 14.5 % / Biso Wilson estimate: 14.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.032 / Net I/σ(I): 15.8 / Num. measured all: 563578 / Scaling rejects: 998
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.0514.70.3187.44518630780.9840.085100
8.94-25.8812.80.0431.166075160.9990.01295.9

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L49

3l49


Resolution: 2→25.8 Å / FOM work R set: 0.828 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 1970 5.11 %Random
Rwork0.1838 36553 --
obs0.1861 38523 92.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.37 Å2 / Biso mean: 17.81 Å2 / Biso min: 1.22 Å2
Refinement stepCycle: final / Resolution: 2→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 25 484 4905
Biso mean--9.95 22.23 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134521
X-RAY DIFFRACTIONf_angle_d1.4896165
X-RAY DIFFRACTIONf_chiral_restr0.08728
X-RAY DIFFRACTIONf_plane_restr0.009801
X-RAY DIFFRACTIONf_dihedral_angle_d15.7321681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05010.26651800.200927842964100
2.0501-2.10550.2468930.18961946203969
2.1055-2.16740.29511550.201127702925100
2.1674-2.23730.38341340.30762607274193
2.2373-2.31720.4138780.35871782186063
2.3172-2.40990.22721620.185627982960100
2.4099-2.51950.24771470.17427952942100
2.5195-2.65220.25651340.172228512985100
2.6522-2.81820.22711370.18342412254986
2.8182-3.03550.23891530.181728272980100
3.0355-3.34040.24391510.179728603011100
3.3404-3.82250.21471170.16732435255285
3.8225-4.81080.15241570.13362714287195
4.8108-25.8840.17011720.152129723144100
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)
12.83040.33211.37091.73390.39342.09490.0504-0.20170.2770.07030.0112-0.09960.01160.0915-0.05590.02850.00970.02770.15260.01630.1485-8.666722.095550.3885
20.1175-0.0327-0.01580.3586-0.16980.18680.0059-0.02870.0579-0.0681-0.0508-0.02640.05290.06850.01680.03670.03420.0070.15360.02510.1274-15.501214.299648.0331
30.71690.1034-0.25190.41810.04480.56590.05150.1489-0.0718-0.1582-0.02660.16090.0784-0.0839-0.04630.10430.0095-0.08130.1176-0.00150.1629-35.28347.565338.5686
43.03430.426-0.75271.30480.14450.7999-0.01780.0689-0.4244-0.1709-0.06810.03210.2502-0.01960.08670.27280.0474-0.0940.13920.00420.1447-33.26293.566832.235
50.68490.0350.3470.7447-0.03521.00190.06230.13440.0565-0.3299-0.0390.04890.20460.0474-0.00430.2120.0543-0.04210.12920.01650.136-28.124915.300830.4057
60.6683-0.08640.73650.6385-0.38062.4937-0.0703-0.04710.3126-0.1048-0.03270.105-0.1534-0.03220.11790.08830.0263-0.04110.18050.00370.2317-28.695425.887842.996
70.5158-0.227-0.25031.8084-0.98321.447-0.04140.10610.1324-0.0489-0.0487-0.2386-0.17110.10970.09090.5347-0.15670.01640.19410.02410.192210.246729.68932.9286
80.42320.4122-0.04460.7121-0.01220.3626-0.04850.09470.0343-0.07110.0407-0.0476-0.19940.1522-0.04150.5443-0.2264-0.01450.27290.0020.155714.735324.94726.5881
90.1301-0.04410.00840.152-0.19360.642-0.0853-0.00390.01180.02480.04450.0138-0.1777-0.0115-0.02430.81690.07170.0490.20070.00350.19341.775432.36765.8505
100.15430.2191-0.04670.8194-0.52640.7137-0.03310.02760.0710.05530.16360.1461-0.2346-0.1291-0.08080.50910.01960.08360.14360.0310.1568-0.357627.7895-2.3618
110.60090.0964-0.04020.2443-0.15320.8630.02280.03340-0.08940.0737-0.0028-0.1496-0.1012-0.09770.15250.0140.01330.09050.00580.08360.39014.54046.0928
121.1032-0.0511-0.22342.33491.43671.0674-0.0308-0.0938-0.0485-0.083-0.06840.3118-0.0823-0.24020.08670.14610.0328-0.01610.19670.03630.1326-6.63253.180715.8572
130.6881-0.2663-0.21710.9942-0.0351.8467-0.0195-0.1238-0.11910.0332-0.00360.0183-0.15690.02030.0120.0580.006-0.01070.10060.010.09443.354.290422.4907
140.20990.4988-0.48551.4971-1.60511.7814-0.10180.1106-0.0689-0.0888-0.1282-0.2522-0.14740.44230.28330.2696-0.10090.03290.20320.01730.144414.011814.01250.7392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 61 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 165 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 197 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 214 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 215 through 308 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 309 through 336 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 61 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 78 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 103 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 104 through 136 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 137 through 197 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 198 through 214 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 215 through 291 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 292 through 332 )B0

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