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- PDB-2id3: Crystal structure of transcriptional regulator SCO5951 from Strep... -

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Basic information

Entry
Database: PDB / ID: 2id3
TitleCrystal structure of transcriptional regulator SCO5951 from Streptomyces coelicolor A3(2)
ComponentsPutative transcriptional regulator
KeywordsTRANSCRIPTION / transcriptional regulator / structural genomics / 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 / metal ion binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain / 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 ...Tetracyclin repressor-like, C-terminal domain / 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: 1.7 Å
AuthorsGrabowski, M. / Chruszcz, M. / Koclega, K.D. / Cymborowski, M. / Gu, J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator
B: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,38413
Polymers47,9572
Non-polymers42711
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-103 kcal/mol
Surface area16360 Å2
MethodPISA
2
A: Putative transcriptional regulator
hetero molecules

A: Putative transcriptional regulator
hetero molecules

B: Putative transcriptional regulator
hetero molecules

B: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,76726
Polymers95,9134
Non-polymers85422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation6_654-x+3/2,-y+1/2,z-1/21
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area5290 Å2
ΔGint-221 kcal/mol
Surface area35280 Å2
MethodPISA
3
A: Putative transcriptional regulator
B: Putative transcriptional regulator
hetero molecules

A: Putative transcriptional regulator
B: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,76726
Polymers95,9134
Non-polymers85422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area10410 Å2
ΔGint-279 kcal/mol
Surface area30070 Å2
MethodPISA
4
A: Putative transcriptional regulator
hetero molecules

A: Putative transcriptional regulator
hetero molecules

B: Putative transcriptional regulator
hetero molecules

B: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,76726
Polymers95,9134
Non-polymers85422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area5520 Å2
ΔGint-195 kcal/mol
Surface area34970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.069, 85.617, 126.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-606-

CA

21B-613-

HOH

31B-813-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 14 - 203 / Label seq-ID: 36 - 225

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative transcriptional regulator


Mass: 23978.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO5951 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 star magic / References: UniProt: O54180
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: 0.1M Tris7.2, 0.2M CaCl2, 30%PEG400, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97904 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: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 48840 / Num. obs: 48644 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.079 / Rsym value: 0.059 / Net I/σ(I): 31.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4651 / Rsym value: 0.399 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
Omodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.291 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19876 2454 5.1 %RANDOM
Rwork0.16437 ---
all0.16607 46137 --
obs0.16607 46137 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--1.52 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 11 481 3308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212915
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9573972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8245393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19921.295139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32515437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7331548
X-RAY DIFFRACTIONr_chiral_restr0.1010.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21452
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22067
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2335
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.215
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1560.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.51942
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34822985
X-RAY DIFFRACTIONr_scbond_it2.53831095
X-RAY DIFFRACTIONr_scangle_it3.8454.5980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1355 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.345
loose thermal1.3410
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 159 -
Rwork0.183 3117 -
obs--91.41 %

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