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- PDB-3npi: Crystal structure of a TetR family regulatory protein (DIP1788) f... -

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Basic information

Entry
Database: PDB / ID: 3npi
TitleCrystal structure of a TetR family regulatory protein (DIP1788) from CORYNEBACTERIUM DIPHTHERIAE at 2.96 A resolution
ComponentsTetR family regulatory protein
KeywordsGENE REGULATION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


HTH-type transcriptional repressor NicS, C-terminal / Tetracyclin repressor-like, C-terminal domain / 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative TetR-family regulatory protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.96 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TetR family regulatory protein (DIP1788) from CORYNEBACTERIUM DIPHTHERIAE at 2.96 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 13, 2013Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: TetR family regulatory protein
B: TetR family regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,20310
Polymers56,4342
Non-polymers7698
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-150 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.238, 137.238, 54.725
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein TetR family regulatory protein


Mass: 28217.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP1788 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6NFU8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.86
Details: 1.7100M ammonium sulfate, 10.0000% Dioxane, 0.1M MES pH 6.86, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97959,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979591
30.979251
ReflectionResolution: 2.96→29.713 Å / Num. obs: 12584 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 99.731 Å2 / Rmerge F obs: 0.115 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.066 / Net I/σ(I): 17.06 / Num. measured all: 93470
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.97-3.080.9470.7431.89695250124960.86399.8
3.08-3.20.6230.4852.89115235523510.56399.8
3.2-3.340.3540.3054.48872227722770.354100
3.34-3.520.2490.2016.69641248124800.234100
3.52-3.740.140.12110.69257237923740.1499.8
3.74-4.020.090.07715.89179235723550.08999.9
4.02-4.430.0510.04923.69568245624510.05699.8
4.43-5.060.0360.0429.49309239323780.04699.4
5.06-6.340.0370.03929.29275238123770.04699.8
6.340.0180.02445.89559249024550.02898.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.96→29.713 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9233 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. SULFATES FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 3.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 609 4.84 %RANDOM
Rwork0.2007 ---
obs0.2016 12572 --
Displacement parametersBiso max: 204.84 Å2 / Biso mean: 97.8883 Å2 / Biso min: 45.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.7305 Å20 Å20 Å2
2--3.7305 Å20 Å2
3----7.461 Å2
Refinement stepCycle: LAST / Resolution: 2.96→29.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 40 0 3205
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1106SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it3254HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion440SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3876SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3254HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4416HARMONIC100.32
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion13.63
LS refinement shellResolution: 2.96→3.24 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2692 141 4.75 %
Rwork0.2426 2826 -
all0.2438 2967 -
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)
12.6951-0.7675-1.16155.84280.45311.0719-0.10340.0177-1.0505-0.3443-0.04840.65040.3282-0.37930.1519-0.2623-0.1397-0.0543-0.1982-0.05220.1291-5.441843.68472.5389
24.4145-1.32650.41983.6865-0.70081.9297-0.1008-0.3978-0.16980.2993-0.0823-0.2188-0.049-0.00470.1831-0.1164-0.0539-0.0529-0.10830.0226-0.17965.329660.06619.7089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A15 - 227
2X-RAY DIFFRACTION2{ B|* }B17 - 251

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