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- PDB-2id6: Crystal structure of transcriptional regulator (tm1030) at 1.75A ... -

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Basic information

Entry
Database: PDB / ID: 2id6
TitleCrystal structure of transcriptional regulator (tm1030) at 1.75A resolution
ComponentsTRANSCRIPTIONAL REGULATOR, TetR FAMILY
KeywordsTRANSCRIPTION / transcriptional regulator / TetR Family
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
: / 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. ...: / 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
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 1.746 Å
AuthorsKoclega, K.D. / Chruszcz, M. / Minor, W.
CitationJournal: To be Published
Title: Crystal structure of transcriptional regulator (tm1030) at 1.75A resolution
Authors: Koclega, K.D. / Chruszcz, M. / Minor, W.
History
DepositionSep 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR, TetR FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4712
Polymers24,4091
Non-polymers621
Water2,720151
1
A: TRANSCRIPTIONAL REGULATOR, TetR FAMILY
hetero molecules

A: TRANSCRIPTIONAL REGULATOR, TetR FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9424
Polymers48,8182
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)55.765, 66.012, 55.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1128-

HOH

21A-1144-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, -y+1, z REMARK 6 transformation matrix: REMARK 6 -1.0 0.0 0.0 | 0.0 REMARK 6 0.0 -1.0 0.0 | 1.0 REMARK 6 0.0 0.0 1.0 | 0.0

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR, TetR FAMILY


Mass: 24409.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1030 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q9X0C0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3%w/v Dextrose, 30%w/v PEG 2K MME, 0.1 M KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.27819 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27819 Å / Relative weight: 1
ReflectionResolution: 1.746→33.83 Å / Num. all: 21489 / Num. obs: 21339 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.062 / Rsym value: 0.061 / Net I/σ(I): 45.9
Reflection shellResolution: 1.746→1.81 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2043 / Rsym value: 0.365 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: isomorphous replacement
Starting model: 1Z77

1z77


Resolution: 1.746→33.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.756 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25102 1091 5.2 %RANDOM
Rwork0.20916 ---
all0.21136 20076 --
obs0.21136 20076 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.746→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 4 151 1812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221693
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9682273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4255205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25623.5881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81415322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7171512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021259
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2823
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21205
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3131.51050
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55121622
X-RAY DIFFRACTIONr_scbond_it3.3553740
X-RAY DIFFRACTIONr_scangle_it4.3794.5650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.746→1.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 87 -
Rwork0.237 1310 -
obs--90.07 %

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