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- PDB-2iai: Crystal structure of SCO3833, a member of the TetR transcriptiona... -

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Basic information

Entry
Database: PDB / ID: 2iai
TitleCrystal structure of SCO3833, a member of the TetR transcriptional regulator family from Streptomyces coelicolor A3
ComponentsPutative transcriptional regulator SCO3833
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TETR / TRANSCRIPTIONAL REGULATOR / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
HTH-type transcriptional repressor KstR2, 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. / Homeodomain-like / Homeobox-like domain superfamily ...HTH-type transcriptional repressor KstR2, 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsZimmerman, M.D. / Xu, X. / Wang, S. / Gu, J. / Chruszcz, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of SCO3833, a member of the TetR transcriptional regulator family from Streptomyces coelicolor A3
Authors: Zimmerman, M.D. / Xu, X. / Wang, S. / Gu, J. / Chruszcz, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Apr 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
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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE, HOWEVER, THAT THIS BIOLOGICAL ASSEMBLY HAS NOT BEEN EXPERIMENTALLY DETERMINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator SCO3833


Theoretical massNumber of molelcules
Total (without water)25,8481
Polymers25,8481
Non-polymers00
Water5,152286
1
A: Putative transcriptional regulator SCO3833

A: Putative transcriptional regulator SCO3833


Theoretical massNumber of molelcules
Total (without water)51,6972
Polymers51,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area21790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.308, 61.308, 113.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

DetailsThe biological assembly has not been experimentally determined. The PITA protein interface prediction server (http://www.ebi.ac.uk/thornton-srv/databases/pita/) predicts that the biological assembly is a dimer, generated from the monomer in the asymmetric unit by the y, x, -z operation.

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Components

#1: Protein Putative transcriptional regulator SCO3833


Mass: 25848.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3 / Gene: SCO3833 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star magic / References: UniProt: Q9XA31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: Crystallized from mother liquor containing 0.1 M Tris-HCl pH=8.5 and 7%(w/v) PEG 8000, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 9, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.65→53.07 Å / Num. all: 30460 / Num. obs: 30460 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.2
Reflection shellResolution: 1.65→1.693 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2212 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
ARP/wARPmodel building
RESOLVEphasing
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.65→53.07 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.016 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CCP4 and COOT software has also been used in the refinement. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 1537 5 %RANDOM
Rwork0.1685 ---
all0.17042 28923 --
obs0.17042 28923 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.489 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.218 Å
Refinement stepCycle: LAST / Resolution: 1.65→53.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 0 286 1845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211718
X-RAY DIFFRACTIONr_bond_other_d0.0020.021673
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9592327
X-RAY DIFFRACTIONr_angle_other_deg0.9233812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0675221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.6620.24183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0815307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4111531
X-RAY DIFFRACTIONr_chiral_restr0.1040.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021970
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
X-RAY DIFFRACTIONr_nbd_refined0.2250.2445
X-RAY DIFFRACTIONr_nbd_other0.20.21765
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2868
X-RAY DIFFRACTIONr_nbtor_other0.0830.21077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2231.51142
X-RAY DIFFRACTIONr_mcbond_other0.3461.5442
X-RAY DIFFRACTIONr_mcangle_it1.63921703
X-RAY DIFFRACTIONr_scbond_it2.9213707
X-RAY DIFFRACTIONr_scangle_it4.1894.5622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 107 -
Rwork0.175 2105 -
obs--100 %
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)
13.998-0.3678-2.41593.35712.30496.513-0.0722-0.1605-0.03470.10280.1495-0.24240.05410.3809-0.0773-0.14140.01990.0133-0.1244-0.0218-0.181730.58811.09-21.337
21.70161.18770.85564.37042.15183.0795-0.26450.18970.1445-0.8150.19530.0617-0.62510.14360.06910.0558-0.0372-0.017-0.11770.0358-0.09145.8771.0338.169
30.65420.6465-0.42111.64770.28230.7547-0.0581-0.0032-0.0033-0.04930.01220.047-0.0203-0.07410.0459-0.0911-0.00710.0001-0.02580.0177-0.068636.074-21.71410.577
42.12632.8318-0.07747.41950.52890.8522-0.06650.0058-0.11980.16370.1414-0.26210.0719-0.0365-0.075-0.09720.0182-0.027-0.07860.012-0.095444.661-25.23216.447
51.66430.07960.18241.6864-0.52251.4035-0.04620.0531-0.0311-0.09780.04980.14760.0787-0.1103-0.0035-0.051-0.0094-0.001-0.0377-0.0009-0.109137.71-29.1980.802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-8 - 513 - 26
2X-RAY DIFFRACTION2AA12 - 6133 - 82
3X-RAY DIFFRACTION3AA62 - 11283 - 133
4X-RAY DIFFRACTION4AA113 - 144134 - 165
5X-RAY DIFFRACTION5AA145 - 207166 - 228

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