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- PDB-3jsj: Crystal structure of a putative tetr-transcriptional regulator (s... -

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Basic information

Entry
Database: PDB / ID: 3jsj
TitleCrystal structure of a putative tetr-transcriptional regulator (sav143) from streptomyces avermitilis ma-4680 at 2.10 A resolution
ComponentsPutative TetR-family transcriptional regulator
KeywordsTRANSCRIPTION / Dna-binding / transcription regulation / bacterial regulatory proteins / dna/rna-binding 3-helical bundle fold / helix turn helix motif / hth motif / transcription regulator / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


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 transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces avermitilis MA-4680 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative transcriptional regulator (NP_821317.1) from Streptomyces avermitilis MA-4680 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Putative TetR-family transcriptional regulator
B: Putative TetR-family transcriptional regulator
C: Putative TetR-family transcriptional regulator
D: Putative TetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9449
Polymers82,6724
Non-polymers2735
Water8,143452
1
A: Putative TetR-family transcriptional regulator
B: Putative TetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5846
Polymers41,3362
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-7 kcal/mol
Surface area16440 Å2
MethodPISA
2
C: Putative TetR-family transcriptional regulator
D: Putative TetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3603
Polymers41,3362
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-26 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.401, 84.351, 103.390
Angle α, β, γ (deg.)90.000, 102.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A6 - 189
2114B6 - 189
3114C6 - 189
4114D6 - 189
DetailsREMARK 300 REMARK 300 REMARK: ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH REMARK 300 STATIC LIGHT SCATTERING SUGGESTS THAT A TETRAMER IS A REMARK 300 SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. HOWEVER, R REMARK 300 ANALYSIS OF THE CRYSTAL PACKING SUGGESTS THAT A DIMER REMARK 300 IS OLIGOMERIZATION STATE IN THE CRYSTAL. REMARK 300 REMARK 300 BIOMOLECULE: 1,2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 BIOMOLECULE 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA FOR THE COMPLEX: 3280 A**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 16490 A**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -20 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA FOR THE COMPLEX: 3300 A**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 16620 A**2 REMARK 350 GAIN IN SOLVENT FREE ENERGY: -20 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein
Putative TetR-family transcriptional regulator


Mass: 20667.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis MA-4680 (bacteria)
Gene: NP_821317.1, SAV143, SAV_143 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q82RK0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THIE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THIE 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3000M magnesium chloride, 16.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97809
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97809 Å / Relative weight: 1
ReflectionResolution: 2.1→29.748 Å / Num. obs: 55159 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.23 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.170.5851.41916910025198.1
2.17-2.260.4531.92140211144198.7
2.26-2.360.3322.52022410513199
2.36-2.490.2653.12165111224199
2.49-2.640.1924.22005210371199
2.64-2.850.1395.72153311118198.9
2.85-3.130.0928.32056610595198.7
3.13-3.590.05114.12115110871198.7
3.59-4.510.03221.12071410618198.4
4.51-29.7480.02625.12103710751197.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.748 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.532 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.168
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. MAGNESIUM FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2802 5.1 %RANDOM
Rwork0.189 ---
obs0.191 55139 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.07 Å2 / Biso mean: 21.447 Å2 / Biso min: 4.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 17 452 5995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225693
X-RAY DIFFRACTIONr_bond_other_d0.0010.023963
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9897705
X-RAY DIFFRACTIONr_angle_other_deg0.98839610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7245756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.08322.96250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.31215957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8871561
X-RAY DIFFRACTIONr_chiral_restr0.0820.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021188
X-RAY DIFFRACTIONr_mcbond_it1.30333694
X-RAY DIFFRACTIONr_mcbond_other0.51631499
X-RAY DIFFRACTIONr_mcangle_it2.27355850
X-RAY DIFFRACTIONr_scbond_it4.27781999
X-RAY DIFFRACTIONr_scangle_it6.68111842
Refine LS restraints NCS

Ens-ID: 1 / Number: 2267 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.250.5
2BMEDIUM POSITIONAL0.290.5
3CMEDIUM POSITIONAL0.320.5
4DMEDIUM POSITIONAL0.30.5
1AMEDIUM THERMAL0.92
2BMEDIUM THERMAL0.782
3CMEDIUM THERMAL0.962
4DMEDIUM THERMAL0.792
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 193 -
Rwork0.24 3845 -
all-4038 -
obs--98.95 %
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)
11.3820.1839-0.20391.1681-0.78761.81170.0066-0.00570.1025-0.0350.00020.0842-0.0258-0.125-0.00680.12830.0087-0.03960.0163-0.00520.0368.72573.5152.102
20.65510.01120.40161.6858-1.57742.9680.05470.08820.0211-0.1236-0.2537-0.20650.15690.40490.19910.11520.0439-0.00060.0790.02750.066387.80160.81358.936
31.16190.711-1.6981.1567-0.63722.8360.1412-0.29550.02350.0525-0.0441-0.0944-0.33960.3583-0.09710.19380.0206-0.05270.34980.0570.106761.68451.124108.339
41.0011-0.46161.06930.8332-1.44235.3963-0.0123-0.2391-0.1468-0.04410.1860.08730.1615-0.5142-0.17370.1212-0.0174-0.03810.19340.10080.12342.57547.0794.916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 189
2X-RAY DIFFRACTION2B6 - 189
3X-RAY DIFFRACTION3C7 - 189
4X-RAY DIFFRACTION4D6 - 189

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