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- PDB-5f7v: ABC substrate-binding protein Lmo0181 from Listeria monocytogenes... -

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Basic information

Entry
Database: PDB / ID: 5f7v
TitleABC substrate-binding protein Lmo0181 from Listeria monocytogenes in complex with cycloalternan
ComponentsLmo0181 protein
KeywordsCYCLOALTERNAN BINDING PROTEIN / substrate-binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyBacterial 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 / Lmo0181 protein
Function and homology information
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLight, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0181 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4592
Polymers44,7921
Non-polymers6671
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint15 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.034, 37.639, 90.426
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lmo0181 protein / Cycloalternan substrate-binding protein


Mass: 44792.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0181 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8YAE9
#2: Polysaccharide Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,4,4/[a2122h-1a_1-5]/1-1-1-1/a1-d6_a3-b1_b6-c1_c3-d1WURCSPDB2Glycan 1.1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.87 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 26 mg/mL protein in 0.05 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 2 mM cycloalternan against Classics II D4 (Qiagen, 0.1 M citric acid, pH 3.5, 25% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 64488 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→29.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.93 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18099 3207 5 %RANDOM
Rwork0.15144 ---
obs0.15293 61269 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.681 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å20.07 Å2
2--0.11 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.4→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 44 546 3678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023384
X-RAY DIFFRACTIONr_bond_other_d0.0010.023048
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9634625
X-RAY DIFFRACTIONr_angle_other_deg1.39237110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12326.826167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49115569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.31152
X-RAY DIFFRACTIONr_chiral_restr0.0970.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.023921
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02743
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_it0.4460.3881644
X-RAY DIFFRACTIONr_mcbond_other0.4460.3881643
X-RAY DIFFRACTIONr_mcangle_it0.7850.582083
X-RAY DIFFRACTIONr_mcangle_other0.7850.582084
X-RAY DIFFRACTIONr_scbond_it0.6980.4451740
X-RAY DIFFRACTIONr_scbond_other0.6980.4451740
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0640.6422543
X-RAY DIFFRACTIONr_long_range_B_refined4.7192.6124567
X-RAY DIFFRACTIONr_long_range_B_other4.7182.6124568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 236 -
Rwork0.202 4458 -
obs--98.34 %
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)
11.74860.12651.05810.85330.51374.0724-0.0112-0.1584-0.03620.14130.0184-0.01310.19880.0671-0.00730.06130.0045-0.00750.04310.00150.036933.6797-8.611391.2916
22.2235-0.1984-0.22350.81460.92745.2483-0.04570.1563-0.16440.1008-0.02850.12410.4845-0.16440.07430.0745-0.04140.01320.0365-0.01090.08525.0939-13.761779.2727
31.015-0.2126-0.69230.04670.14023.3896-0.01630.01-0.03990.00680.00010.02150.0868-0.35340.01630.031-0.01370.00760.0671-0.00360.089822.8109-4.59676.7655
44.69310.27391.35182.11310.92255.6980.0319-0.17260.3436-0.0041-0.05810.0755-0.2941-0.13090.02610.0360.02420.01530.0355-0.0110.089324.93627.372183.9351
50.914-0.9003-0.69591.47160.82061.21780.0337-0.07820.07780.00050.028-0.0224-0.11450.0362-0.06170.0292-0.007-0.00940.017-0.00520.038739.0175-0.801272.5402
62.12-1.80181.74922.7751-1.59852.83640.00260.03250.0869-0.0227-0.0485-0.10110.05750.2090.04590.02770.0070.01050.0247-0.00430.024252.1461-12.5952.3953
70.3865-0.1618-0.0550.30830.05520.3054-0.0105-0.0038-0.01910.00870.00410.01710.03080.00090.00640.0154-0.002-0.00540.00050.00250.028439.7202-13.580657.4969
82.34-0.3638-0.9340.79530.36411.6794-0.0194-0.19230.04970.06890.0555-0.0010.03830.1157-0.03610.0245-0.0014-0.00880.0416-0.00190.030835.6116-2.405384.8714
90.9229-0.35790.82970.1389-0.31172.6488-0.0776-0.09420.18330.030.0372-0.073-0.18470.14340.04050.0484-0.0151-0.02330.0524-0.02230.080651.5414-3.170971.588
100.4234-0.04020.15790.60280.150.67010.02-0.0352-0.0077-0.0012-0.00490.066-0.0259-0.0753-0.01510.00640.0004-0.00330.01740.00030.04523.1902-8.229654.8753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 62
2X-RAY DIFFRACTION2A63 - 79
3X-RAY DIFFRACTION3A80 - 101
4X-RAY DIFFRACTION4A102 - 117
5X-RAY DIFFRACTION5A118 - 158
6X-RAY DIFFRACTION6A159 - 175
7X-RAY DIFFRACTION7A176 - 300
8X-RAY DIFFRACTION8A301 - 343
9X-RAY DIFFRACTION9A344 - 370
10X-RAY DIFFRACTION10A371 - 418

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