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- PDB-3eet: Crystal structure of putative GntR-family transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 3eet
TitleCrystal structure of putative GntR-family transcriptional regulator
ComponentsPutative GntR-family transcriptional regulator
Keywordstranscription regulator / GntR-family transcriptional regulator / Streptomyces avermitilis / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family ...UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative GntR-family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.969 Å
AuthorsChang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative GntR-family transcriptional regulator from Streptomyces avermitilis
Authors: Chang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative GntR-family transcriptional regulator
B: Putative GntR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)60,4112
Polymers60,4112
Non-polymers00
Water3,873215
1
A: Putative GntR-family transcriptional regulator

A: Putative GntR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)60,4112
Polymers60,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3840 Å2
ΔGint-22 kcal/mol
Surface area23100 Å2
MethodPISA
2
B: Putative GntR-family transcriptional regulator

B: Putative GntR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)60,4112
Polymers60,4112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
Buried area3540 Å2
ΔGint-19 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.157, 87.157, 123.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Detailschain A make dimer with operator y,x,-z+1 chang B make dimer with operator -x+2,-x+y+1,-z

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Components

#1: Protein Putative GntR-family transcriptional regulator


Mass: 30205.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: SAV3189, SAV_3189 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q82IF8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Na formate,20%PEG3350, 1/400 thermolysin w/w, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
Reflection twinOperator: h+k,-h,l / Fraction: 0.172
ReflectionResolution: 1.969→50 Å / Num. obs: 74259 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 48.8
Reflection shellResolution: 1.97→1.99 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.45 / Num. unique all: 987 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.969→36.198 Å / σ(F): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2182 3728 5.02 %
Rwork0.1761 --
all0.1782 74259 -
obs0.1782 74259 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.36 Å2 / ksol: 0.328 e/Å3
Refinement stepCycle: LAST / Resolution: 1.969→36.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 0 215 3903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.923
X-RAY DIFFRACTIONf_dihedral_angle_deg15.255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9693-2.00330.28791860.25533418X-RAY DIFFRACTION98
2.0033-2.03970.29031990.25263562X-RAY DIFFRACTION98
2.0397-2.07890.26841820.24813564X-RAY DIFFRACTION98
2.0789-2.12140.28292080.2393504X-RAY DIFFRACTION98
2.1214-2.16750.26631650.23013563X-RAY DIFFRACTION98
2.1675-2.21790.25042100.21863486X-RAY DIFFRACTION98
2.2179-2.27340.26031780.24323474X-RAY DIFFRACTION98
2.2734-2.33480.25651760.21723590X-RAY DIFFRACTION98
2.3348-2.40350.27071680.21743563X-RAY DIFFRACTION98
2.4035-2.48110.20781760.20893557X-RAY DIFFRACTION98
2.4811-2.56970.25671910.21673535X-RAY DIFFRACTION98
2.5697-2.67260.22681730.22223512X-RAY DIFFRACTION98
2.6726-2.79420.21791890.21253554X-RAY DIFFRACTION98
2.7942-2.94140.27472080.20913496X-RAY DIFFRACTION98
2.9414-3.12560.22411820.19763540X-RAY DIFFRACTION98
3.1256-3.36680.23121710.17983582X-RAY DIFFRACTION98
3.3668-3.70530.21772130.16073494X-RAY DIFFRACTION98
3.7053-4.24070.18192130.12763500X-RAY DIFFRACTION98
4.2407-5.34010.14021740.10853564X-RAY DIFFRACTION98
5.3401-36.20380.22611660.14943473X-RAY DIFFRACTION98
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)
11.05390.5088-0.45712.6483-2.46032.49010.0404-0.1466-0.02110.0204-0.4199-0.2752-0.16610.31240.30510.27460.0232-0.01590.22850.04730.307520.576926.133879.4046
2-0.2658-0.0247-0.05220.703-0.11441.7766-0.034-0.235-0.04960.0954-0.0187-0.1692-0.02110.60020.08550.1960.0103-0.01450.29060.01960.288839.87549.91958.877
32.63570.1759-1.66561.03181.6789-0.04740.1368-0.0576-0.4768-0.41710.0978-0.117-0.0414-0.0139-0.14890.3480.05810.02020.2949-0.01520.346937.538244.695240.709
41.7808-0.0206-0.20931.08980.04680.79870.15920.4115-0.0361-0.3064-0.1108-0.0708-0.07420.0489-0.03130.29440.05660.04550.31590.01360.255134.762652.803841.2735
51.3329-0.1662-0.2122-1.00560.23910.94770.11520.0499-0.06250.0126-0.06670.0281-0.071-0.0438-0.06510.21330.0176-0.00560.1992-0.02050.253329.095148.189351.4369
61.2212-1.1693-0.67652.37091.9962.1888-0.576-0.02360.043-1.2259-0.57331.5774-1.2405-0.14260.62070.8189-0.0388-0.47370.354-0.09980.884868.032422.1229-16.8696
70.14420.2718-0.62630.8179-0.51350.8187-0.07580.1830.0351-0.21630.21490.13020.049-0.47-0.08550.3737-0.0452-0.04640.4913-0.03030.286149.516446.16372.9206
82.10851.38960.71361.33591.43662.28940.2370.1362-0.07140.27180.0904-0.02780.58860.2403-0.23650.4425-0.0018-0.02810.37070.01120.299753.038841.380722.1463
90.65290.0666-0.13630.69160.56322.6227-0.0505-0.172-0.0007-0.05160.03730.0224-0.4445-0.1090.0340.32220.0110.00310.3251-0.01690.238354.620449.311620.6933
101.00730.49160.45170.28150.20071.6470.04280.2231-0.0973-0.090.0823-0.1002-0.30250.2173-0.07610.316-0.0297-0.01550.3429-0.04010.256260.189744.60379.8447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1-72
2X-RAY DIFFRACTION2chain A and (resid 77-103 or resid 239-250)
3X-RAY DIFFRACTION3chain A and resid 104-115
4X-RAY DIFFRACTION4chain A and resid 116-186
5X-RAY DIFFRACTION5chain A and resid 187-238
6X-RAY DIFFRACTION6chain B and resid 1-72
7X-RAY DIFFRACTION7chain B and (resid 77-103 or resid 239-250)
8X-RAY DIFFRACTION8chain B and resid 104-115
9X-RAY DIFFRACTION9chain B and resid 116-186
10X-RAY DIFFRACTION10chain B and resid 187-238

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