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- PDB-2wv1: CRYSTAL STRUCTURE OF THE HLYIIR MUTANT PROTEIN WITH RESIDUES 169-... -

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Basic information

Entry
Database: PDB / ID: 2wv1
TitleCRYSTAL STRUCTURE OF THE HLYIIR MUTANT PROTEIN WITH RESIDUES 169-186 SUBSTITUTED BY A LINKER CONTAINING TWO THROMBIN SITES
ComponentsHEMOLYSIN II REGULATORY PROTEIN
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / TETR FAMILY
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
HTH-type transcriptional repressor NicS, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type ...HTH-type transcriptional repressor NicS, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Hemolysin II regulatory protein
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKovalevskiy, O.V. / Solonin, A.S. / Antson, A.A.
CitationJournal: Proteins / Year: 2010
Title: Structural Investigation of Transcriptional Regulator Hlyiir: Influence of a Disordered Region on Protein Fold and Dimerization.
Authors: Kovalevskiy, O.V. / Solonin, A.S. / Antson, A.A.
History
DepositionOct 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HEMOLYSIN II REGULATORY PROTEIN
B: HEMOLYSIN II REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1553
Polymers46,0932
Non-polymers621
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-27 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.315, 70.473, 139.238
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 HEMOLYSIN II REGULATORY PROTEIN


Mass: 23046.434 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-168,187-201
Source method: isolated from a genetically manipulated source
Details: SEGMENT 169-186 SUBSTITUTED BY A LINKER CONTAINING TWO THROMBIN SITES
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: B771 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q7X506
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEGMENT 169-186 SUBSTITUTED BY A LINKER CONTAINING TWO THROMBIN SITES

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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: 3.06 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 7.5 / Details: TRIS, SODIUM NITRATE, PEG3350, pH 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 23639 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0097refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FX0

2fx0


Resolution: 2.3→24.73 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.895 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. U VALUES RESIDUAL ONLY. LINKER REGION WAS CUT OFF USING THROMBIN
RfactorNum. reflection% reflectionSelection details
Rfree0.23613 1194 5.1 %RANDOM
Rwork0.18705 ---
obs0.18951 22337 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.202 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2---1.53 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 4 155 3156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9594170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9775369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36224.733150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32715581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6451510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212316
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.72831830
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.13752955
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.25181270
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.802121211
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.423 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.325 175 -
Rwork0.238 3185 -
obs--99.7 %
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)
13.25121.78860.675814.3934-2.47743.12460.1343-0.16680.3171-0.5361-0.01620.3089-0.11190.013-0.11810.310.01830.04620.0164-0.01110.1122-17.30920.769-13.226
21.72490.2111-0.76582.5316-0.24141.95240.0566-0.00840.2965-0.01790.0478-0.1958-0.2356-0.0215-0.10440.22060.0017-0.00870.0863-0.00630.0903-18.405-3.194-0.074
35.36522.9005-4.10595.2793-3.240613.51150.17240.08570.0826-0.0845-0.0259-0.0563-0.05970.1759-0.14650.4569-0.00930.05610.16070.08340.0573-9.039-1.338-36.292
42.8654-0.138-0.07372.2263-0.60882.1748-0.00460.30630.0193-0.297-0.079-0.07090.01280.07270.08360.2138-0.01580.02150.07880.0090.0175-12.692-16.528-14.249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 66
2X-RAY DIFFRACTION2A68 - 198
3X-RAY DIFFRACTION3B4 - 66
4X-RAY DIFFRACTION4B67 - 198

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