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- PDB-4n4u: Crystal structure of ABC transporter solute binding protein BB071... -

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Basic information

Entry
Database: PDB / ID: 4n4u
TitleCrystal structure of ABC transporter solute binding protein BB0719 from Bordetella bronchiseptica RB50, TARGET EFI-510049
ComponentsPutative ABC transporter periplasmic solute-binding protein
KeywordsTRANSPORT PROTEIN / ABC PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter periplasmic solute-binding protein / Putative ABC transporter periplasmic solute-binding protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsPatskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ABC transporter periplasmic solute-binding protein
B: Putative ABC transporter periplasmic solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2933
Polymers71,2012
Non-polymers921
Water8,809489
1
A: Putative ABC transporter periplasmic solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6932
Polymers35,6011
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ABC transporter periplasmic solute-binding protein


Theoretical massNumber of molelcules
Total (without water)35,6011
Polymers35,6011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.568, 68.532, 153.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.367686, -0.096368, 0.924943), (-0.306009, 0.926687, 0.218195), (-0.87816, -0.363268, 0.311241)5.5078, 39.44881, 67.34068

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Components

#1: Protein Putative ABC transporter periplasmic solute-binding protein / ABC TRANSPORTER PERIPLASMIC SOLUTE BINDING PROTEIN


Mass: 35600.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: BB0719 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WPG5, UniProt: A0A0H3LMU1*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.23 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: PROTEIN IN 10 MM HEPES, PH 7.5, 150 MM SODIUM CHLORIDE, 5% GLYCEROL, RESERVOIR: 0.1M BIS-TRIS:HCL, 28% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2013 / Details: MIRRORS
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 168537 / % possible obs: 99.5 % / Observed criterion σ(I): -5 / Redundancy: 5 % / Biso Wilson estimate: 20.18 Å2 / Rsym value: 0.065 / Net I/σ(I): 11.9
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.8 / % possible all: 92.2

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.95 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2661 3 %RANDOM
Rwork0.176 ---
obs0.177 85398 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-0 Å20 Å2
2---0.68 Å20 Å2
3---3.15 Å2
Refinement stepCycle: LAST / Resolution: 1.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 6 489 5117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194857
X-RAY DIFFRACTIONr_bond_other_d0.0010.024734
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9676586
X-RAY DIFFRACTIONr_angle_other_deg0.77310901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09123.889216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1415849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5291539
X-RAY DIFFRACTIONr_chiral_restr0.0780.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021115
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6581.612464
X-RAY DIFFRACTIONr_mcbond_other3.6581.612463
X-RAY DIFFRACTIONr_mcangle_it4.0312.6943087
X-RAY DIFFRACTIONr_mcangle_other4.0312.6943088
X-RAY DIFFRACTIONr_scbond_it5.9112.1552393
X-RAY DIFFRACTIONr_scbond_other5.9112.1552393
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1963.3593479
X-RAY DIFFRACTIONr_long_range_B_refined9.5848.9415970
X-RAY DIFFRACTIONr_long_range_B_other9.5088.0995679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 193 -
Rwork0.281 6168 -
obs--98.6 %
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)
10.9021-0.50280.03991.47760.13740.14260.07350.13370.0722-0.1179-0.0779-0.1108-0.013-0.01140.00440.132-0.00150.00770.07850.0010.012315.385467.801434.5251
22.38560.0547-0.45971.291-0.64811.3578-0.01980.4795-0.2754-0.1577-0.0874-0.04610.24770.16920.10720.25720.0303-0.00240.3054-0.04440.035423.800537.14765.135
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 326
2X-RAY DIFFRACTION2B25 - 326

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