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- PDB-2hyt: CRYSTAL STRUCTURE OF A TETR-FAMILY TRANSCRIPTIONAL REGULATOR (ECA... -

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Basic information

Entry
Database: PDB / ID: 2hyt
TitleCRYSTAL STRUCTURE OF A TETR-FAMILY TRANSCRIPTIONAL REGULATOR (ECA1819) FROM PECTOBACTERIUM ATROSEPTICUM AT 1.64 A RESOLUTION
ComponentsTetR-family transcriptional regulator
KeywordsTRANSCRIPTION / TETR-FAMILY TRANSCRIPTIONAL REGULATOR / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TetR-family transcriptional regulator
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of TetR-family transcriptional regulator (YP_049917.1) from Erwinia Cartovora Atroseptica SCRI1043 at 1.64 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ASSIGNMENT OF A DIMER AS THE BIOLOGICAL UNIT IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3356
Polymers22,0251
Non-polymers3105
Water5,260292
1
A: TetR-family transcriptional regulator
hetero molecules

A: TetR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,67112
Polymers44,0502
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)82.858, 82.858, 56.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

DetailsASSIGNMENT OF A DIMER AS THE BIOLOGICAL UNIT IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY.

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Components

#1: Protein TetR-family transcriptional regulator


Mass: 22025.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: YP_049917.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6D668
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Description: THE STRUCTURE WAS INITIALLY SOLVED BY MAD FROM ONE CRYSTAL AND REFINEMENT WAS AGAINST DATA FROM A SECOND HIGHER RESOLUTION CRYSTAL
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.2
Details: 0.2M NH4F, 20.0% PEG-3350, No Buffer pH 6.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.000001
SYNCHROTRONSSRL BL11-120.979197,0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2006 / 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
11.0000011
20.9791971
30.918371
ReflectionResolution: 1.6→27.126 Å / Num. obs: 27542 / % possible obs: 100 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.64-1.685.80.79811140019730.79899.9
1.68-1.735.80.6831.11150319890.68399.9
1.73-1.785.80.5151.51101118870.515100
1.78-1.835.80.4051.91086518620.405100
1.83-1.895.90.3422.21054918000.342100
1.89-1.965.80.2532.91026817630.253100
1.96-2.035.90.1913.9976816690.191100
2.03-2.128.40.2023.41379216330.202100
2.12-2.2111.10.17341729015540.173100
2.21-2.32110.1464.61641114980.146100
2.32-2.44110.125.71577014280.12100
2.44-2.59110.0966.91465913350.096100
2.59-2.7710.90.0857.51393312800.085100
2.77-2.9910.90.0787.61271911720.078100
2.99-3.2810.80.0659.11196011080.065100
3.28-3.6710.60.069.9105879960.06100
3.67-4.2310.10.05311.289888910.053100
4.23-5.1910.60.05411.180907610.054100
5.19-7.3310.60.05111.763215990.051100
7.33-28.048.60.04312.329573440.04397.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.64→27.126 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.26 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.089
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1386 5 %RANDOM
Rwork0.163 ---
obs0.165 27537 99.93 %-
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: 18.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å20 Å2
2--0.61 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.64→27.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 20 292 1774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221577
X-RAY DIFFRACTIONr_bond_other_d0.0020.021088
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9782145
X-RAY DIFFRACTIONr_angle_other_deg0.90732647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0795222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41723.64974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73815276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1191517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_nbd_refined0.2520.2346
X-RAY DIFFRACTIONr_nbd_other0.2050.21174
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2784
X-RAY DIFFRACTIONr_nbtor_other0.0890.2831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.226
X-RAY DIFFRACTIONr_mcbond_it2.39531077
X-RAY DIFFRACTIONr_mcbond_other0.5263409
X-RAY DIFFRACTIONr_mcangle_it2.76251599
X-RAY DIFFRACTIONr_scbond_it4.6588609
X-RAY DIFFRACTIONr_scangle_it6.47511531
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 104 -
Rwork0.216 1880 -
obs-1984 99.9 %
Refinement TLS params.Method: refined / Origin x: 22.46 Å / Origin y: 41.354 Å / Origin z: 12.35 Å
111213212223313233
T-0.0176 Å20.0272 Å20.0011 Å2-0.004 Å20.0016 Å2--0.0344 Å2
L0.0853 °20.1253 °2-0.1518 °2-0.1992 °2-0.1739 °2--0.4291 °2
S0.0353 Å °-0.0427 Å °0.0043 Å °0.0015 Å °-0.0321 Å °0.0171 Å °-0.0022 Å °0.0392 Å °-0.0032 Å °
Refinement TLS groupSelection: ALL

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