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- PDB-4r6k: Crystal structure of ABC transporter substrate-binding protein Ye... -

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Basic information

Entry
Database: PDB / ID: 4r6k
TitleCrystal structure of ABC transporter substrate-binding protein YesO from Bacillus subtilis, TARGET EFI-510761, an open conformation
ComponentsSOLUTE-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / Sugar transporter / SBP-type / Enzyme Function Initiative / EFI / structural genomics
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Putative ABC transporter substrate-binding protein YesO
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.94 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of transporter Yeso from Bacillus subtilis, Target Efi-510761
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _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_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: SOLUTE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6952
Polymers48,6721
Non-polymers231
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.932, 75.727, 119.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SOLUTE-BINDING PROTEIN


Mass: 48671.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU06970 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31518
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growpH: 7.5
Details: Protein: 10 mM BIS-TRIS, 500 mm NaCl, 5% glycerol, 5 mm DTT; reservoir: 1.4 m sodium citrate, 0.1 m HEPES-NaOH, pH 7.5; vapor diffusion, sitting drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2014 / Details: MIRRORS
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 30836 / % possible obs: 99.3 % / Observed criterion σ(I): -5 / Redundancy: 6.9 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 25
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.78 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHASERphasing
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 2DVU

2dvu


Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.057 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25981 952 3.1 %RANDOM
Rwork0.1918 ---
obs0.19383 29819 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.652 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å2-0 Å2
2---2.18 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 1 202 3382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023252
X-RAY DIFFRACTIONr_bond_other_d0.0010.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9664402
X-RAY DIFFRACTIONr_angle_other_deg0.79137125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84925.769156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89315585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3091510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
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_it7.5284.0151583
X-RAY DIFFRACTIONr_mcbond_other7.5174.0141582
X-RAY DIFFRACTIONr_mcangle_it7.6386.2561977
X-RAY DIFFRACTIONr_mcangle_other7.646.261978
X-RAY DIFFRACTIONr_scbond_it13.4345.0611669
X-RAY DIFFRACTIONr_scbond_other13.4345.061670
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.7277.3712426
X-RAY DIFFRACTIONr_long_range_B_refined13.65615.4594002
X-RAY DIFFRACTIONr_long_range_B_other13.71915.2853924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 64 -
Rwork0.298 2020 -
obs--92.83 %
Refinement TLS params.Method: refined / Origin x: 17.8583 Å / Origin y: 29.1701 Å / Origin z: 25.6041 Å
111213212223313233
T0.1285 Å20.0166 Å2-0.027 Å2-0.0214 Å2-0.0065 Å2--0.0164 Å2
L0.5338 °20.1858 °2-0.3154 °2-0.8242 °2-0.7359 °2--1.9139 °2
S0.0046 Å °-0.0057 Å °-0.0637 Å °0.0367 Å °-0.0126 Å °-0.0393 Å °-0.0534 Å °-0.0171 Å °0.008 Å °

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