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- PDB-5ydp: Crystal Structure of TetR Family Repressor AlkX from Dietzia sp. ... -

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Basic information

Entry
Database: PDB / ID: 5ydp
TitleCrystal Structure of TetR Family Repressor AlkX from Dietzia sp. Strain DQ12-45-1b Implicated in Biodegradation of n-Alkanes
ComponentsTetR transcriptional regulatory protein
KeywordsGENE REGULATION / 10 alfa helices / homodimer / apo-protein
Function / homologyTetracyclin repressor C-terminal, Actinobacteria / Bacterial Tetracyclin repressor, C-terminal domain / : / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / TetR transcriptional regulatory protein
Function and homology information
Biological speciesDietzia sp. DQ12-45-1b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.091 Å
AuthorsZheng, H. / Gao, Y. / Liang, J.L.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: Crystal Structure of TetR Family Repressor AlkX from Dietzia sp. Strain DQ12-45-1b Implicated in Biodegradation ofn-Alkanes.
Authors: Liang, J.L. / Gao, Y. / He, Z. / Nie, Y. / Wang, M. / JiangYang, J.H. / Zhang, X.C. / Shu, W.S. / Wu, X.L.
History
DepositionSep 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR transcriptional regulatory protein
B: TetR transcriptional regulatory protein
C: TetR transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)78,6653
Polymers78,6653
Non-polymers00
Water00
1
A: TetR transcriptional regulatory protein
B: TetR transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)52,4432
Polymers52,4432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-15 kcal/mol
Surface area17400 Å2
MethodPISA
2
C: TetR transcriptional regulatory protein

C: TetR transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)52,4432
Polymers52,4432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2570 Å2
ΔGint-13 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.662, 179.711, 56.646
Angle α, β, γ (deg.)90.000, 110.520, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))
21(chain B and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))
31(chain C and (resid 31 through 156 or resid 158 through 214))

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILE(chain A and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))AA31 - 12547 - 141
12LEULEU(chain A and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))AA135 - 156151 - 172
13GLNGLN(chain A and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))AA158 - 214174 - 230
21ILEILE(chain B and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))BB31 - 12547 - 141
22LEULEU(chain B and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))BB135 - 156151 - 172
23GLNGLN(chain B and (resid 31 through 125 or resid 135 through 156 or resid 158 through 214))BB158 - 214174 - 230
31LEULEU(chain C and (resid 31 through 156 or resid 158 through 214))CC31 - 15647 - 172
32GLNGLN(chain C and (resid 31 through 156 or resid 158 through 214))CC158 - 214174 - 230

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Components

#1: Protein TetR transcriptional regulatory protein / AlkX


Mass: 26221.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dietzia sp. DQ12-45-1b (bacteria) / Gene: AlkwR / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G3EIL4
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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01M magnesium acetate, 0.05M Sodium cacodylate, 1.3M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979622 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 18667 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 32.74 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.102 / Χ2: 1.146 / Net I/av σ(I): 18.481 / Net I/σ(I): 10 / Num. measured all: 119304
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.216.50.48218530.9220.2070.5251.0299.2
3.21-3.346.40.3590.9480.1550.3921.06599.2
3.34-3.496.50.2570.9730.110.28199.5
3.49-3.686.50.1780.9840.0770.1941.01299.4
3.68-3.916.40.1260.9910.0540.1370.95599.5
3.91-4.216.40.1040.9930.0450.1130.99499.6
4.21-4.636.40.0890.9940.0380.0970.98599.7
4.63-5.36.40.0810.9950.0350.0891.09799.6
5.3-6.676.30.0850.9930.0370.0931.40699.7
6.67-506.20.0620.9970.0270.0681.96298.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.091→34.152 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 28.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2825 918 4.99 %
Rwork0.2453 17472 -
obs0.2472 18390 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.9 Å2 / Biso mean: 26.345 Å2 / Biso min: 2.55 Å2
Refinement stepCycle: final / Resolution: 3.091→34.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 0 0 4172
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134252
X-RAY DIFFRACTIONf_angle_d1.4915763
X-RAY DIFFRACTIONf_chiral_restr0.068678
X-RAY DIFFRACTIONf_plane_restr0.009740
X-RAY DIFFRACTIONf_dihedral_angle_d6.743279
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2324X-RAY DIFFRACTION12.387TORSIONAL
12B2324X-RAY DIFFRACTION12.387TORSIONAL
13C2324X-RAY DIFFRACTION12.387TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0911-3.25390.3351300.31442392252294
3.2539-3.45760.38271210.29282458257997
3.4576-3.72430.30431340.26992501263598
3.7243-4.09850.25361320.22442510264299
4.0985-4.69030.26291320.2172536266899
4.6903-5.90430.28121360.24652522265899
5.9043-34.15360.22591330.20542553268698

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