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- PDB-4ich: Crystal structure of a putative TetR family transcriptional regul... -

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Basic information

Entry
Database: PDB / ID: 4ich
TitleCrystal structure of a putative TetR family transcriptional regulator from Saccharomonospora viridis DSM 43017
ComponentsTranscriptional regulator
KeywordsTranscription Regulator / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / transcriptional regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix 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 ...BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix 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. / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / BROMIDE ION / Transcriptional regulator
Similarity search - Component
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative TetR family transcriptional regulator from Saccharomonospora viridis DSM 43017
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4289
Polymers71,5032
Non-polymers9257
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-10 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.845, 76.929, 109.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999985, 0.000341, -0.005392), (5.5E-5, -0.997307, -0.073346), (-0.005402, -0.073345, 0.997292)43.87046, 156.16573, 5.89664

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcriptional regulator


Mass: 35751.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Strain: DSM 43017 / Gene: Svir_16270 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: C7MT25

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Non-polymers , 5 types, 135 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium Bromide, 0.1 M Bis Tris propane, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2012 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 50916 / Num. obs: 50916 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 42.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2515 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→28.64 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.993 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24705 1359 5 %RANDOM
Rwork0.19858 ---
obs0.20101 25724 99.61 %-
all-25724 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.588 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--1.27 Å2-0 Å2
3----1.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 33 128 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193300
X-RAY DIFFRACTIONr_bond_other_d0.0080.023219
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9444461
X-RAY DIFFRACTIONr_angle_other_deg1.9323.0017316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7755390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.50622.26177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3615574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3181546
X-RAY DIFFRACTIONr_chiral_restr0.1180.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023718
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02842
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.947→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 90 -
Rwork0.231 1809 -
obs--97.69 %
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)
12.56960.30880.65752.90941.4596.2548-0.03620.1648-0.0634-0.11530.07320.12390.0866-0.3309-0.0370.13330.0204-0.00960.05450.01990.085510.56867.419121.2367
20.941-0.2855-0.80031.15780.02252.11080.12250.0039-0.07870.01410.01630.05460.0194-0.1578-0.13880.044-0.021-0.01530.02230.00870.08339.319170.904545.6121
32.1629-0.4601-1.09512.22030.05252.470.1414-0.3129-0.06440.0778-0.061-0.0280.07970.3207-0.08040.0704-0.0203-0.04240.06630.01130.094522.004969.034752.1724
47.3718-0.52251.50784.23420.22897.74230.29150.73890.3487-0.1733-0.071-0.19060.08580.7645-0.22050.12970.07660.03110.14220.01880.044833.093187.463621.7983
51.1132-0.66570.59261.42690.0852.13840.22830.01960.0818-0.1071-0.0803-0.0719-0.03440.2393-0.1480.0854-0.01640.03460.0504-0.0150.101734.053583.216541.9439
61.936-0.91511.70192.3683-0.40823.21020.0312-0.27910.03120.3173-0.00720.1869-0.0622-0.1426-0.02390.0863-0.04110.05530.0616-0.02220.057626.481781.43956.2949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 142
2X-RAY DIFFRACTION2A143 - 243
3X-RAY DIFFRACTION3A244 - 284
4X-RAY DIFFRACTION4B95 - 141
5X-RAY DIFFRACTION5B142 - 221
6X-RAY DIFFRACTION6B222 - 285

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