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- PDB-4rsm: Crystal structure of carbohydrate transporter msmeg_3599 from myc... -

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Basic information

Entry
Database: PDB / ID: 4rsm
TitleCrystal structure of carbohydrate transporter msmeg_3599 from mycobacterium smegmatis str. mc2 155, target efi-510970, in complex with d-threitol
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS / HYDROLASE
Function / homology
Function and homology information


cellular response to carbohydrate stimulus / carbohydrate utilization / carbohydrate transport / carbohydrate binding / plasma membrane
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
D-Threitol / D-threitol-binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Siedel, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis.
Authors: Huang, H. / Carter, M.S. / Vetting, M.W. / Al-Obaidi, N. / Patskovsky, Y. / Almo, S.C. / Gerlt, J.A.
History
DepositionNov 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Structure summary
Revision 1.2Jun 10, 2015Group: Non-polymer description
Revision 1.3Jun 1, 2016Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Feb 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: Periplasmic binding protein/LacI transcriptional regulator
B: Periplasmic binding protein/LacI transcriptional regulator
C: Periplasmic binding protein/LacI transcriptional regulator
D: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8758
Polymers137,3864
Non-polymers4884
Water16,033890
1
A: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4692
Polymers34,3471
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4692
Polymers34,3471
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4692
Polymers34,3471
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4692
Polymers34,3471
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.723, 128.288, 66.579
Angle α, β, γ (deg.)90.00, 93.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99407, 0.000145, -0.108743), (-0.003984, -0.999376, 0.035087), (-0.108671, 0.035312, 0.99345)93.85368, 47.56119, 37.13964
3given(0.022406, 0.023505, -0.999473), (-0.004322, 0.999717, 0.023414), (0.99974, 0.003795, 0.022501)123.75078, -33.44855, 5.23508
4given(0.065067, -0.027769, -0.997495), (-0.038663, -0.998932, 0.025287), (-0.997132, 0.036921, -0.066071)89.74874, 17.05028, 98.869

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Components

#1: Protein
Periplasmic binding protein/LacI transcriptional regulator / Sugar-binding transcriptional regulator / LacI family protein


Mass: 34346.574 Da / Num. of mol.: 4 / Fragment: UNP residues 25-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3599, MSMEI_3516 / Plasmid: pet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QYB5
#2: Chemical
ChemComp-3VB / D-Threitol


Mass: 122.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 1.95 Å3/Da / Density % sol: 36.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-THREITOL), RESERVOIR: 0.1 M CITRIC ACID:NAOH, PH 4.0, 25% PEG3350, CRYOPROTECTION: RESERVOIR SOLUTION, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 126794 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 23.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.5 / % possible all: 90.7

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Processing

Software
NameVersionClassification
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.948 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21738 3974 3 %RANDOM
Rwork0.17678 ---
obs0.17805 126794 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.245 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0 Å2-0.5 Å2
2---2.63 Å2-0 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9270 0 32 890 10192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199514
X-RAY DIFFRACTIONr_bond_other_d0.0010.029292
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.97212927
X-RAY DIFFRACTIONr_angle_other_deg0.948321427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01251284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08327.213409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56151641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3141531
X-RAY DIFFRACTIONr_chiral_restr0.2460.21514
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111127
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021896
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_it3.7181.5635061
X-RAY DIFFRACTIONr_mcbond_other3.7181.5635060
X-RAY DIFFRACTIONr_mcangle_it4.0792.6116328
X-RAY DIFFRACTIONr_mcangle_other4.0792.6116329
X-RAY DIFFRACTIONr_scbond_it8.5122.1394453
X-RAY DIFFRACTIONr_scbond_other8.5122.1394453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8393.2596586
X-RAY DIFFRACTIONr_long_range_B_refined9.3628.23411517
X-RAY DIFFRACTIONr_long_range_B_other9.4397.76111082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 270 -
Rwork0.228 8918 -
obs--90.38 %
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)
11.05930.1355-0.05441.6231-0.51490.9011-0.05080.07650.00220.0062-0.0387-0.1931-0.08610.05340.08950.0142-0.0052-0.00220.09210.00840.028563.749413.828949.3812
22.7497-0.21361.06531.9333-0.13551.93450.11450.02490.0376-0.1174-0.02560.25760.0221-0.2086-0.08890.01750.01710.00040.14590.02410.065928.609134.223414.3456
30.6108-0.3014-0.07592.4501-0.05991.0190.03850.08980.0042-0.4279-0.0490.2177-0.0012-0.04450.01050.08080.0123-0.0330.0927-0.00450.029342.570446.042762.0997
40.8592-0.45390.22521.89460.03741.3420.01560.0968-0.0727-0.1865-0.0092-0.03340.13720.0558-0.00650.0417-0.00630.01510.1271-0.00740.019847.75682.070929.0194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 325
2X-RAY DIFFRACTION2B33 - 325
3X-RAY DIFFRACTION3C33 - 324
4X-RAY DIFFRACTION4D34 - 325

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