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- PDB-6hyh: Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in c... -

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Basic information

Entry
Database: PDB / ID: 6hyh
TitleCrystal structure of MSMEG_1712 from Mycobacterium smegmatis in complex with Beta-D-Fucofuranose
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein
Function / homology
Function and homology information


cell envelope / carbohydrate binding / metal ion binding
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-fucofuranose / ABC transporter periplasmic-binding protein YtfQ / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, M. / Mueller, C. / Zhang, L. / Einsle, O. / Jessen-Trefzer, C.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Detection and Characterization of a Mycobacterial L-Arabinofuranose ABC Transporter Identified with a Rapid Lipoproteomics Protocol.
Authors: Li, M. / Muller, C. / Frohlich, K. / Gorka, O. / Zhang, L. / Gross, O. / Schilling, O. / Einsle, O. / Jessen-Trefzer, C.
History
DepositionOct 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,57817
Polymers67,3992
Non-polymers1,17915
Water48627
1
A: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules

A: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,15534
Polymers134,7984
Non-polymers2,35730
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455-x-1,-y,z1
Buried area8630 Å2
ΔGint-823 kcal/mol
Surface area45680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.065, 118.065, 232.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-511-

HOH

31B-505-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 17 - 320 / Label seq-ID: 16 - 319

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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Components

#1: Protein Periplasmic binding protein/LacI transcriptional regulator


Mass: 33699.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_1672 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7G686, UniProt: A0QT50*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-GYE / beta-D-fucofuranose / beta-D-fucose / 6-deoxy-beta-D-galactofuranose / D-fucose / fucose


Type: D-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
DfucfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fucofuranoseCOMMON NAMEGMML 1.0
b-D-FucfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium chloride, magnesium chloride, Tris pH 7.5, PEG 1500

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→83.485 Å / Num. obs: 28372 / % possible obs: 99.9 % / Redundancy: 27.1 % / Biso Wilson estimate: 63.02 Å2 / Net I/σ(I): 10.4
Reflection shellResolution: 2.512→2.806 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HBD

6hbd


Resolution: 2.5→52.62 Å / SU ML: 0.2432 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3069
RfactorNum. reflection% reflection
Rfree0.2379 936 4.83 %
Rwork0.2109 --
obs0.2123 19397 67.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→52.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 35 27 4628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01034670
X-RAY DIFFRACTIONf_angle_d1.3896340
X-RAY DIFFRACTIONf_chiral_restr0.0701720
X-RAY DIFFRACTIONf_plane_restr0.0091848
X-RAY DIFFRACTIONf_dihedral_angle_d8.43392802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.640.3509120.461251X-RAY DIFFRACTION6.59
2.64-2.80.3592400.3934648X-RAY DIFFRACTION17.07
2.8-3.020.3709920.33891851X-RAY DIFFRACTION48.2
3.02-3.320.29891750.30073829X-RAY DIFFRACTION98.74
3.32-3.80.26352090.22733876X-RAY DIFFRACTION99.88
3.8-4.790.19891880.18013924X-RAY DIFFRACTION100
4.79-52.630.21482200.17724082X-RAY DIFFRACTION99.65

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