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- PDB-6hb0: Crystal structure of MSMEG_1712 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6hb0
TitleCrystal structure of MSMEG_1712 from Mycobacterium smegmatis
ComponentsABC transporter periplasmic-binding protein YtfQ
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein
Function / homology
Function and homology information


carbohydrate 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
ABC transporter periplasmic-binding protein YtfQ
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, M. / Mueller, C. / 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
DepositionAug 9, 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 1.2May 15, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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.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.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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,18320
Polymers68,0062
Non-polymers1,17718
Water4,954275
1
A: ABC transporter periplasmic-binding protein YtfQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,65711
Polymers34,0031
Non-polymers65410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter periplasmic-binding protein YtfQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5269
Polymers34,0031
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.746, 75.746, 186.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 16 - 320 / Label seq-ID: 18 - 322

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein ABC transporter periplasmic-binding protein YtfQ


Mass: 34002.820 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)
Gene: MSMEG_1712 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QT50
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3,350, zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→65.6 Å / Num. obs: 47434 / % possible obs: 99.97 % / Redundancy: 20.2 % / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.94 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→65.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.027 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22185 2488 5 %RANDOM
Rwork0.17883 ---
obs0.181 47434 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.583 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å2-0 Å2
2---0.12 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.9→65.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 18 275 4786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194614
X-RAY DIFFRACTIONr_bond_other_d0.0010.024246
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9456266
X-RAY DIFFRACTIONr_angle_other_deg0.84939877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02525.822213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77515748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5761519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
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_it3.0383.7582418
X-RAY DIFFRACTIONr_mcbond_other3.0353.7582417
X-RAY DIFFRACTIONr_mcangle_it4.2045.6163023
X-RAY DIFFRACTIONr_mcangle_other4.2055.6163024
X-RAY DIFFRACTIONr_scbond_it4.0564.1892196
X-RAY DIFFRACTIONr_scbond_other4.0514.1882196
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2416.0963242
X-RAY DIFFRACTIONr_long_range_B_refined8.61646.215321
X-RAY DIFFRACTIONr_long_range_B_other8.63246.0715260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9131 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 198 -
Rwork0.282 3443 -
obs--99.92 %

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