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- PDB-4r6h: Crystal structure of putative binding protein msme from bacillus ... -

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Basic information

Entry
Database: PDB / ID: 4r6h
TitleCrystal structure of putative binding protein msme from bacillus subtilis subsp. subtilis str. 168, target efi-510764, an open conformation
ComponentsSolute binding protein MsmE
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / SBP-TYPE / EFI / STRUCTURAL GENOMICS / Enzyme Function Initiative
Function / homology
Function and homology information


polysaccharide transport / plasma membrane
Similarity search - Function
: / 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
Similarity search - Domain/homology
Melibiose/raffinose/stachyose-binding protein MelE
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 Msme from Bacillus Subtilis, Target Efi-510764
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 1.1Feb 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

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Assembly

Deposited unit
A: Solute binding protein MsmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8756
Polymers48,6981
Non-polymers1775
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.736, 61.920, 114.708
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 MsmE


Mass: 48697.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: msmE, BSU30270 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34335
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 5% GLYCEROL, 5 MM DTT; RESERVOIR: 1.0 M LITHIUM CHLORIDE, 0.1 M SODIUM CITRATE:HCL, PH 4.0, 20% PEG6000, 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: Apr 28, 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: 1.5→57.35 Å / Num. obs: 63410 / % possible obs: 98.4 % / Observed criterion σ(I): -5 / Redundancy: 6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 25.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / Rsym value: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→57.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.499 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20501 1915 3 %RANDOM
Rwork0.16784 ---
obs0.16898 61428 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0 Å2
2--0.23 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→57.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 5 466 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023312
X-RAY DIFFRACTIONr_bond_other_d0.0010.023136
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9584500
X-RAY DIFFRACTIONr_angle_other_deg0.83237253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.285415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27324.907161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9021516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
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_it3.5133.0171600
X-RAY DIFFRACTIONr_mcbond_other3.513.0131599
X-RAY DIFFRACTIONr_mcangle_it4.3445.0722005
X-RAY DIFFRACTIONr_mcangle_other4.3515.0782006
X-RAY DIFFRACTIONr_scbond_it9.0413.6991712
X-RAY DIFFRACTIONr_scbond_other9.0393.7051713
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1715.8492486
X-RAY DIFFRACTIONr_long_range_B_refined10.20312.294288
X-RAY DIFFRACTIONr_long_range_B_other10.26611.8814035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 144 -
Rwork0.241 4512 -
obs--98.23 %

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