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- PDB-3hyj: Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA -

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Basic information

Entry
Database: PDB / ID: 3hyj
TitleCrystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA
ComponentsProtein DUF199/WhiA
KeywordsTRANSCRIPTION REGULATOR / LAGLIDADG / homing endonuclease / helix-turn-helix / HTH
Function / homology
Function and homology information


regulation of sporulation / cell division / DNA binding
Similarity search - Function
Sporulation regulator WhiA / Sporulation transcription regulator WhiA, N-terminal domain / Sporulation regulator WhiA, C-terminal / WhiA, LAGLIDADG-like domain / WhiA C-terminal HTH domain / WhiA N-terminal LAGLIDADG-like domain / WhiA LAGLIDADG-like domain / Homing endonucleases / Endonuclease I-creI / Homing endonuclease ...Sporulation regulator WhiA / Sporulation transcription regulator WhiA, N-terminal domain / Sporulation regulator WhiA, C-terminal / WhiA, LAGLIDADG-like domain / WhiA C-terminal HTH domain / WhiA N-terminal LAGLIDADG-like domain / WhiA LAGLIDADG-like domain / Homing endonucleases / Endonuclease I-creI / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Probable cell division protein WhiA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.6 Å
AuthorsKaiser, B.K. / Clifton, M.C. / Shen, B.W. / Stoddard, B.L.
CitationJournal: Structure / Year: 2009
Title: The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease.
Authors: Kaiser, B.K. / Clifton, M.C. / Shen, B.W. / Stoddard, B.L.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Protein DUF199/WhiA
D: Protein DUF199/WhiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4727
Polymers46,1942
Non-polymers2785
Water1,02757
1
A: Protein DUF199/WhiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2123
Polymers23,0971
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein DUF199/WhiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2604
Polymers23,0971
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.448, 79.899, 115.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein DUF199/WhiA


Mass: 23097.018 Da / Num. of mol.: 2
Fragment: N-terminal domain, generated by proteolytic digestion of the full-length protein (UNP residues 1 to 198)
Source method: isolated from a genetically manipulated source
Details: the expressed protein does not contain any affinity tags.
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: MSB8, TM_1708 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9X234
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris, 9.0, 20% Ethanol, 200 mM NaCl. Crystals of the N-terminal domain were generated by the addition of trypsin to the full-length protein just prior to setting crystal drops., VAPOR ...Details: 0.1 M Tris, 9.0, 20% Ethanol, 200 mM NaCl. Crystals of the N-terminal domain were generated by the addition of trypsin to the full-length protein just prior to setting crystal drops., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: R-AXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2008 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15039 / Num. obs: 14107 / % possible obs: 93.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 6.35 / % possible all: 89

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHASERphasing
REFMAC5.5.0072refinement
Hdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→40.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 24.914 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.894 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26038 712 5.1 %RANDOM
Rwork0.19823 ---
obs0.20132 13375 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.642 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---0.14 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 15 57 3066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223061
X-RAY DIFFRACTIONr_bond_other_d0.0010.022076
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9754131
X-RAY DIFFRACTIONr_angle_other_deg1.07635051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2015382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45623.095126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15315533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3531520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
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_it0.5351.51911
X-RAY DIFFRACTIONr_mcbond_other0.0851.5775
X-RAY DIFFRACTIONr_mcangle_it1.00523069
X-RAY DIFFRACTIONr_scbond_it1.41631150
X-RAY DIFFRACTIONr_scangle_it2.4254.51061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.604→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 53 -
Rwork0.291 988 -
obs--95.68 %
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)
12.05850.6528-0.01454.80090.2193.16560.10080.05330.0974-0.3148-0.002-0.0029-0.31290.0283-0.09880.2875-0.02960.10220.0107-0.03750.20019.21730.12117.234
22.4816-0.16860.02913.56571.55573.92780.0032-0.2425-0.16810.08810.1812-0.18920.080.0654-0.18440.2503-0.01720.01470.0333-0.00080.19189.59424.31433.144
34.20370.5065-0.61662.46010.59623.8252-0.0072-0.26690.00270.35350.1144-0.01470.10310.2112-0.10720.3095-0.04390.0080.0478-0.01240.145822.94641.3228.047
42.11190.0839-1.07412.93460.62793.9156-0.0126-0.01880.0325-0.10220.13780.0178-0.10760.1751-0.12520.33480.00230.00040.0127-0.00980.225126.16841.296-5.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 98
2X-RAY DIFFRACTION2A99 - 192
3X-RAY DIFFRACTION3D1 - 77
4X-RAY DIFFRACTION4D78 - 193

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