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Basic information

Entry
Database: PDB / ID: 4ryk
TitleCrystal structure of a putative transcriptional regulator from Listeria monocytogenes EGD-e
ComponentsLmo0325 protein
KeywordsDNA BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Transcription activator MutR, C-terminal / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
sucrose / DI(HYDROXYETHYL)ETHER / L(+)-TARTARIC ACID / Lmo0325 protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative transcriptional regulator from Listeria monocytogenes EGD-e
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0325 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4424
Polymers36,8441
Non-polymers5993
Water2,450136
1
A: Lmo0325 protein
hetero molecules

A: Lmo0325 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8858
Polymers73,6882
Non-polymers1,1976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_566x,-y+1,-z+3/21
Buried area7850 Å2
ΔGint-24 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.310, 103.930, 112.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Lmo0325 protein


Mass: 36843.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo0325 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q8YA39
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{}LINUCSPDB-CARE
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M Ammonium Tartrate, 25 % Sucrose, 10 % PEG 400, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Jul 21, 2014 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.09→56.4 Å / Num. all: 30178 / Num. obs: 30178 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.1
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 3 / Num. unique all: 2187 / % possible all: 98.1

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0069refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→56.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 8.317 / SU ML: 0.104 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19919 1514 5 %RANDOM
Rwork0.16783 ---
obs0.1694 28664 99.29 %-
all-28664 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.718 Å2
Baniso -1Baniso -2Baniso -3
1-3.22 Å20 Å2-0 Å2
2---0.56 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.09→56.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 29 136 2648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192574
X-RAY DIFFRACTIONr_bond_other_d0.0010.022442
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9573461
X-RAY DIFFRACTIONr_angle_other_deg0.85135608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97123.778135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2515465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2151517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02635
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_it2.7533.6061182
X-RAY DIFFRACTIONr_mcbond_other2.7443.6051181
X-RAY DIFFRACTIONr_mcangle_it4.0985.3791474
X-RAY DIFFRACTIONr_mcangle_other4.1015.3811475
X-RAY DIFFRACTIONr_scbond_it4.194.1891390
X-RAY DIFFRACTIONr_scbond_other4.194.1891390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3846.11988
X-RAY DIFFRACTIONr_long_range_B_refined8.51330.2553185
X-RAY DIFFRACTIONr_long_range_B_other8.51230.2673186
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 98 -
Rwork0.271 2089 -
obs--98.07 %
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)
12.8129-0.45960.53641.4792-0.40592.94270.06420.02010.15850.0714-0.0748-0.0629-0.02460.62630.01060.1826-0.0052-0.00460.2215-0.00110.010572.99349.633495.3704
22.06470.46431.18265.98870.40251.82870.0523-0.23370.21740.5027-0.0021-0.07440.0750.0851-0.05010.2256-0.00770.06940.0693-0.06370.085659.84672.290777.0757
37.2922-5.37050.004712.4352-2.71819.0444-0.277-0.09510.0627-0.33670.40640.7216-0.2575-0.7498-0.12940.21190.02310.00980.0885-0.04340.298647.280581.920170.0895
42.04670.34170.39270.13190.53283.22580.06470.14280.2149-0.0783-0.00860.0194-0.3792-0.0956-0.05610.25420.05430.03790.07830.01710.027655.358264.623761.9993
52.89330.257-0.58060.61160.11681.5992-0.00630.40940.0156-0.19190.11830.15910.1095-0.1837-0.1120.1908-0.0284-0.04850.12520.05280.066240.455453.975369.895
62.8127-0.6061.63892.6389-0.08284.708-0.19770.04160.21780.00050.14320.3516-0.5531-0.52730.05450.13480.0483-0.03840.13620.10660.18128.408462.394977.3739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 68
2X-RAY DIFFRACTION2A69 - 115
3X-RAY DIFFRACTION3A116 - 134
4X-RAY DIFFRACTION4A135 - 177
5X-RAY DIFFRACTION5A178 - 261
6X-RAY DIFFRACTION6A262 - 297

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