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- PDB-4d5c: tetracycline repressor class J, apo form -

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Basic information

Entry
Database: PDB / ID: 4d5c
Titletetracycline repressor class J, apo form
ComponentsTETRACYCLINE REPRESSOR PROTEIN TETR
KeywordsTRANSCRIPTION / INDUCTION / ALLOSTERY
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, 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 ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, 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
Repressor protein / :
Similarity search - Component
Biological speciesPROTEUS MIRABILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPalm, G.J. / Quast, J. / Hinrichs, W.
CitationJournal: To be Published
Title: Domain Movement in Tetracycline Repressor Classes
Authors: Palm, G.J. / Quast, J. / Hinrichs, W.
History
DepositionNov 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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: TETRACYCLINE REPRESSOR PROTEIN TETR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3782
Polymers23,2821
Non-polymers961
Water3,459192
1
A: TETRACYCLINE REPRESSOR PROTEIN TETR
hetero molecules

A: TETRACYCLINE REPRESSOR PROTEIN TETR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7574
Polymers46,5652
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5380 Å2
ΔGint-64.8 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.150, 106.060, 70.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

21A-2092-

HOH

31A-2187-

HOH

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Components

#1: Protein TETRACYCLINE REPRESSOR PROTEIN TETR / TETRACYCLINE REPRESSOR CLASS J


Mass: 23282.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROTEUS MIRABILIS (bacteria) / Plasmid: PWH610K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RB791 / References: UniProt: S5UX16, UniProt: Q9ZI84*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: MODEL NOT DEPOSITED
Crystal growpH: 7
Details: 1.0 M (NH4)2SO4, 0.07 M NACL, 0.05 M HEPES PH 7.0; CRYO 1.0 M (NH4)2SO4, 0.07 M NACL, 0.05 M HEPES PH 7.0, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Oct 2, 2014 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 21903 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.7
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2 / % possible all: 71.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→53.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.154 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19722 1094 5 %RANDOM
Rwork0.17364 ---
obs0.17486 20809 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.203 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20 Å2
2---4.83 Å20 Å2
3---2.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→53.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 5 192 1725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191592
X-RAY DIFFRACTIONr_bond_other_d0.0010.021519
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9542166
X-RAY DIFFRACTIONr_angle_other_deg0.85733491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8355202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.07425.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.978156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
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_it1.3240.877787
X-RAY DIFFRACTIONr_mcbond_other1.30.873786
X-RAY DIFFRACTIONr_mcangle_it2.141.293984
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7151.084805
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.703→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 67 -
Rwork0.257 1113 -
obs--71.08 %
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)
13.00570.16780.13860.2905-0.08980.052-0.0178-0.13650.0214-0.0059-0.0028-0.0543-0.0005-0.01740.02060.00180.00960.00620.4466-0.00520.034138.64813.718-8.304
23.3870.1558-0.43571.4045-0.02690.50130.0388-0.0845-0.0535-0.0083-0.0662-0.12110.04480.03020.02740.0062-0.00170.0030.37310.01530.020722.9967.512-7.538
31.1975-0.4865-0.21722.92170.14150.6151-0.0272-0.0688-0.0073-0.1535-0.0076-0.11680.03840.07350.03480.0150.01690.01290.43280.01920.012716.7871.7-3.858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 74
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION2A75 - 107
4X-RAY DIFFRACTION3A108 - 208

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