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- PDB-4rk9: CRYSTAL STRUCTURE OF SUGAR TRANSPORTER BL01359 FROM Bacillus lich... -

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Entry
Database: PDB / ID: 4rk9
TitleCRYSTAL STRUCTURE OF SUGAR TRANSPORTER BL01359 FROM Bacillus licheniformis, TARGET EFI-510856, IN COMPLEX WITH STACHYOSE
ComponentsCarbohydrate ABC transporter substrate-binding protein MsmE
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS / STACHYOSE
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
: / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Multiple sugar-binding protein MsmE
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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 SUGAR TRANSPORTER BL01359 FROM Bacillus licheniformis, TARGET EFI-510856
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
DepositionOct 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate ABC transporter substrate-binding protein MsmE
B: Carbohydrate ABC transporter substrate-binding protein MsmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3244
Polymers90,9902
Non-polymers1,3332
Water3,279182
1
A: Carbohydrate ABC transporter substrate-binding protein MsmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1622
Polymers45,4951
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbohydrate ABC transporter substrate-binding protein MsmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1622
Polymers45,4951
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.332, 85.916, 132.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A0 - 415
2114B0 - 415

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.878379, -0.448801, -0.164404), (-0.457961, 0.691789, 0.558301), (-0.136833, 0.56569, -0.813186)-18.61191, 32.11844, -52.17369

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Components

#1: Protein Carbohydrate ABC transporter substrate-binding protein MsmE / Multiple sugar-binding protein MsmE


Mass: 45495.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: DSM 13 / ATCC 14580 / Gene: msmE, BL01359, BLi01140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65LL6
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose-(1-6)-[beta-D-fructofuranose-(2-1)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-6DGalpa1-6[DFrufb2-1]DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3-3/a2-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{[(6+1)][a-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO, 10 MM STACHYOSE; RESERVOIR: 0.1M MAGNESIUM CHLORIDE, 0.1M SODIUM ACETATE:HCL, PH 4.6, 25% PEG 400; ...Details: PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO, 10 MM STACHYOSE; RESERVOIR: 0.1M MAGNESIUM CHLORIDE, 0.1M SODIUM ACETATE:HCL, PH 4.6, 25% PEG 400; CRYOPROTECTION: RESERVOIR, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2014 / Details: MIRRORS
RadiationMonochromator: ROCK CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 47047 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 27.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.202 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27161 1404 3 %RANDOM
Rwork0.19432 ---
obs0.19668 45491 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.926 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å2-0 Å2
2--0.79 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 90 182 6432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026402
X-RAY DIFFRACTIONr_bond_other_d0.0020.025974
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9858678
X-RAY DIFFRACTIONr_angle_other_deg0.772313871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20925.623297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.639151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0921519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021352
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_it10.8975.6723070
X-RAY DIFFRACTIONr_mcbond_other10.8955.673069
X-RAY DIFFRACTIONr_mcangle_it11.2728.4713834
X-RAY DIFFRACTIONr_mcangle_other11.2718.4723835
X-RAY DIFFRACTIONr_scbond_it16.2366.9343332
X-RAY DIFFRACTIONr_scbond_other16.2346.9353333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.2929.8264845
X-RAY DIFFRACTIONr_long_range_B_refined16.04521.177560
X-RAY DIFFRACTIONr_long_range_B_other16.08921.0847506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6019 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.410.5
MEDIUM THERMAL6.975
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 85 -
Rwork0.288 3318 -
obs--99.94 %
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)
13.0469-0.11360.42551.3047-0.21943.9212-0.0837-0.0974-0.04880.0714-0.0186-0.2330.30990.47320.10230.06410.00970.03540.1032-0.03130.0992-25.770513.8567-20.5105
22.5293-0.10570.35882.79190.46884.7646-0.04550.3196-0.0661-0.2109-0.29870.5634-0.1486-0.5520.34420.04370.00340.00670.1762-0.17160.273510.36988.5383-34.7451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 415
2X-RAY DIFFRACTION2B37 - 415

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