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- PDB-5f7r: ROK repressor Lmo0178 from Listeria monocytogenes bound to inducer -

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Basic information

Entry
Database: PDB / ID: 5f7r
TitleROK repressor Lmo0178 from Listeria monocytogenes bound to inducer
ComponentsLmo0178 protein
KeywordsTRANSCRIPTION / Repressor / open reading frame / kinase / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


D-xylose metabolic process / metal ion binding
Similarity search - Function
ROK family / ROK family / Winged helix-turn-helix DNA-binding / ATPase, nucleotide binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Lmo0178 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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 / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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_conn_type.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
E: Lmo0178 protein
A: Lmo0178 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2419
Polymers90,1892
Non-polymers1,0527
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-20 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.200, 95.064, 117.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules EA

#1: Protein Lmo0178 protein / Rok repressor


Mass: 45094.297 Da / Num. of mol.: 2
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: lmo0178 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8YAF1
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 269 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.77 Å3/Da / Density % sol: 30.34 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 9.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II D6 (Qiagen, 0.1 M Bis-Tris, pH 5.5, 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: 1.8→30 Å / Num. obs: 55352 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.1
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure

Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.098 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20029 2664 4.8 %RANDOM
Rwork0.16659 ---
obs0.1682 52630 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 61 264 5056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194999
X-RAY DIFFRACTIONr_bond_other_d0.0010.024749
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9656772
X-RAY DIFFRACTIONr_angle_other_deg0.76310957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5225.133226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91315855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4651517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025712
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021141
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_it1.071.7982500
X-RAY DIFFRACTIONr_mcbond_other1.0691.7972499
X-RAY DIFFRACTIONr_mcangle_it1.7542.6843139
X-RAY DIFFRACTIONr_mcangle_other1.7542.6853140
X-RAY DIFFRACTIONr_scbond_it1.4542.0522499
X-RAY DIFFRACTIONr_scbond_other1.4422.052495
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3782.9853628
X-RAY DIFFRACTIONr_long_range_B_refined5.26315.2015788
X-RAY DIFFRACTIONr_long_range_B_other5.26315.2065789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 204 -
Rwork0.226 3811 -
obs--99.36 %
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)
14.4234-4.11561.03346.6942-1.71181.8519-0.03050.04440.026-0.2476-0.0729-0.43930.14840.35170.10340.08950.0530.06750.1040.00350.096449.05579.768787.989
22.7661-1.34970.56745.5647-1.22263.6336-0.09140.2935-0.2395-0.36040.06250.01660.20950.1040.02890.15280.0160.04940.0705-0.04170.072444.116775.978280.9788
30.9823-0.6855-0.42342.33940.58321.601-0.0771-0.0272-0.1470.0292-0.01490.10240.17770.07570.0920.05060.00940.03990.0358-0.00230.066535.546286.96695.9077
410.08760.3158-1.38325.4125-3.82162.85170.1580.45610.8211-0.3213-0.1797-0.1910.1130.04990.02170.49180.04420.08470.17260.09050.255439.5486113.457585.5271
57.11852.0383-0.20756.1114-1.85536.19130.170.12570.2171-0.3082-0.1713-0.6121-0.30210.3890.00120.1216-0.07260.08280.1060.02960.191147.8025109.179388.4956
60.9684-0.6151-0.54231.590.68271.9486-0.0579-0.24060.04730.03340.1541-0.20350.06980.3952-0.09630.01090.01120.00890.1437-0.01550.07944.104195.1455104.4693
72.8440.4488-0.77361.68540.61043.3156-0.131-0.5427-0.13680.21740.01140.1310.31520.25310.11950.09780.08980.05550.18160.07220.040221.519497.0404133.6458
811.47014.7233-11.3615.1721-2.982412.3591-0.55910.2963-0.85070.2588-0.1629-0.02851.1032-0.36070.7220.590.0484-0.20360.1575-0.10410.642516.500982.4105115.5036
91.1277-0.5547-0.15982.267-0.50811.9583-0.1035-0.1533-0.04830.00020.10260.0351-0.0350.11450.0010.04390.02280.01550.05340.00350.020424.8185104.0566113.0964
101.0784-0.66-0.23292.1772-0.21351.1527-0.09790.0063-0.09430.03660.14370.2558-0.132-0.28-0.04570.03780.03960.00560.11050.02170.064212.7384106.4081109.1219
111.7802-0.4263-1.69831.17770.64745.4584-0.17370.2333-0.33740.0632-0.07640.25320.3475-0.67770.250.0278-0.03980.04130.0935-0.0140.141215.926592.429110.0505
1210.4769-7.3274.553710.4066-8.42357.17890.545-0.3906-0.3222-0.6398-0.03160.56670.48280.1108-0.51340.23160.04380.01730.07920.08110.206822.070880.2246132.2078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 113
2X-RAY DIFFRACTION2A114 - 147
3X-RAY DIFFRACTION3A148 - 270
4X-RAY DIFFRACTION4A271 - 287
5X-RAY DIFFRACTION5A288 - 312
6X-RAY DIFFRACTION6A313 - 391
7X-RAY DIFFRACTION7E83 - 201
8X-RAY DIFFRACTION8E202 - 213
9X-RAY DIFFRACTION9E214 - 279
10X-RAY DIFFRACTION10E280 - 348
11X-RAY DIFFRACTION11E349 - 386
12X-RAY DIFFRACTION12E387 - 391

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