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- PDB-2ras: Crystal structure of a putative tetr/acrr family transcriptional ... -

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Basic information

Entry
Database: PDB / ID: 2ras
TitleCrystal structure of a putative tetr/acrr family transcriptional regulator (saro_0558) from novosphingobium aromaticivorans dsm at 1.80 A resolution
ComponentsTranscriptional regulator, TetR familyTranscriptional regulation
KeywordsTRANSCRIPTION / Bacterial regulatory proteins / tetr family / dna-binding / dna/rna-binding 3-helical bundle fold / helix turn helix motif / hth motif / transcription regulator / transcription regulation / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Tetracyclin repressor-like, C-terminal domain 27 / Tetracyclin repressor-like, C-terminal domain / Cro/C1-type helix-turn-helix domain / Tetracycline Repressor, domain 2 / 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
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of predicted transcriptional regulator of TetR/AcrR family (YP_495839.1) from Novosphingobium aromaticivorans DSM 12444 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,55918
Polymers48,6202
Non-polymers94016
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.500, 76.420, 104.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Transcriptional regulator, TetR family / Transcriptional regulation


Mass: 24309.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: YP_495839.1, Saro_0558 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2GAW8
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: NANODROP, 0.2M MgCl2, 20.0% PEG 3350, No Buffer pH 5.8, 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: 0.91837, 0.97925, 0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979251
30.979011
ReflectionResolution: 1.8→29.709 Å / Num. obs: 47914 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.39 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 14.01
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.4322127568152193.9
1.86-1.940.3282.7153449736198
1.94-2.030.223.8145729220198.3
2.03-2.130.1495.6135818548198.2
2.13-2.270.0998.1151569539198.3
2.27-2.440.0711.1141528782198.3
2.44-2.690.0514.4148809230197.8
2.69-3.070.03320.9144708814197.1
3.07-3.870.01931.9149168919195.9
3.87-29.7090.01641.2147518519191.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.709 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.258 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107
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. RESIDUES 1-4 IN BOTH CHAINS, 205-211 IN CHAIN A, AND 209-211 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 6. THERE ARE UNEXPLAINED DENSITIES NEAR GLU-121 SUGGESTING A MG ION COORDINATED BY WATERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2413 5 %RANDOM
Rwork0.177 ---
obs0.178 47877 98.77 %-
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: 34.359 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2---0.23 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 58 353 3544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223342
X-RAY DIFFRACTIONr_bond_other_d0.0040.022311
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9644517
X-RAY DIFFRACTIONr_angle_other_deg1.42735571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5345438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.823.072166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94915558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2511536
X-RAY DIFFRACTIONr_chiral_restr0.0940.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023796
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02736
X-RAY DIFFRACTIONr_nbd_refined0.1920.2716
X-RAY DIFFRACTIONr_nbd_other0.1450.22378
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21645
X-RAY DIFFRACTIONr_nbtor_other0.0750.21640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.225
X-RAY DIFFRACTIONr_mcbond_it1.77732131
X-RAY DIFFRACTIONr_mcbond_other0.4113839
X-RAY DIFFRACTIONr_mcangle_it2.57153290
X-RAY DIFFRACTIONr_scbond_it4.45981379
X-RAY DIFFRACTIONr_scangle_it6.269111209
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 161 -
Rwork0.25 3271 -
all-3432 -
obs--96.51 %
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)
11.2931-0.4127-1.04220.98750.35231.838-0.02690.05190.0904-0.07670.1236-0.19790.07030.0717-0.0967-0.2051-0.0177-0.011-0.1563-0.0313-0.109614.14418.22420.71
20.8706-0.44580.46441.33770.17272.4724-0.02760.01190.0059-0.1250.06180.1824-0.1444-0.2241-0.0342-0.1968-0.01240.0008-0.1760.0074-0.1369-13.36829.61222.246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2046 - 205
2X-RAY DIFFRACTION2BB5 - 2086 - 209

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