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Basic information

Entry
Database: PDB / ID: 3elk
TitleCrystal structure of putative transcriptional regulator TA0346 from Thermoplasma acidophilum
ComponentsPutative transcriptional regulator TA0346
Keywordstranscription regulator / transcriptional regulator / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like 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 / Mainly Alpha / Transcription regulator PadR N-terminal domain-containing protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsGrantz Saskova, K. / Chruszcz, M. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative transcriptional regulator TA0346 from Thermoplasma acidophilum
Authors: Grantz Saskova, K. / Chruszcz, M. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
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_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

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Assembly

Deposited unit
A: Putative transcriptional regulator TA0346
B: Putative transcriptional regulator TA0346
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3294
Polymers27,2582
Non-polymers712
Water2,324129
1
A: Putative transcriptional regulator TA0346
B: Putative transcriptional regulator TA0346
hetero molecules

A: Putative transcriptional regulator TA0346
B: Putative transcriptional regulator TA0346
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6588
Polymers54,5164
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6570 Å2
ΔGint-82 kcal/mol
Surface area23270 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.515, 45.707, 207.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative transcriptional regulator TA0346


Mass: 13629.079 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0346 / Plasmid: P15TV LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q9HL84
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M AMMONIUM SULFATE, 0.1M NA SULFATE PH4.6, 30% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2008 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 21233 / Num. obs: 21233 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 40.646
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1004 / Rsym value: 0.452 / % possible all: 88

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
SHELXEmodel building
RESOLVEmodel building
ARP/wARPmodel building
CCP4model building
REFMAC5.4.0069refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.57 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1099 5.2 %RANDOM
Rwork0.202 ---
all0.204 21126 --
obs0.204 21126 92.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.16 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å20 Å20 Å2
2--0.32 Å20 Å2
3----3.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 2 129 1761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221653
X-RAY DIFFRACTIONr_bond_other_d0.0090.021120
X-RAY DIFFRACTIONr_angle_refined_deg2.0331.9922224
X-RAY DIFFRACTIONr_angle_other_deg3.32332766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9685204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.99724.76263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49515328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.143156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021753
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02297
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_it1.1041.51026
X-RAY DIFFRACTIONr_mcbond_other0.3981.5424
X-RAY DIFFRACTIONr_mcangle_it1.88121648
X-RAY DIFFRACTIONr_scbond_it3.9123627
X-RAY DIFFRACTIONr_scangle_it5.2824.5576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 79 -
Rwork0.215 1392 -
obs--87.98 %
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)
12.291-0.2169-1.02072.1908-1.35916.79610.2020.02770.09950.0779-0.22390.00790.0060.43340.0219-0.10740.04380.0049-0.06930.006-0.015516.5931.20791.847
215.9592-7.2268-8.189410.53311.59179.72610.30940.33060.77730.12290.0073-0.0637-0.4944-0.151-0.3168-0.06960.1050.016-0.08730.03970.020511.8968.9785.009
328.9843-0.3537-6.535310.370.9441.6838-1.0646-1.44861.04851.18060.9305-0.34720.00660.27540.1340.11870.1561-0.0881-0.024-0.0373-0.076814.19212.28792.172
49.5162-3.62483.004414.43670.4856.264-0.2956-0.1370.30090.24710.2421-0.6688-0.17490.3220.0534-0.10550.0328-0.0248-0.053-0.00510.001926.6984.06889.133
51.5348-0.36051.836813.1133-8.58187.297-0.00160.30090.2136-0.2538-0.1508-0.1296-0.13070.61710.15230.00380.09980.06990.05920.07390.047124.9197.7376.366
61.1342-0.3771-1.5910.99690.2724.8916-0.10490.0345-0.1141-0.0074-0.09360.04280.4403-0.19450.1985-0.12580.0519-0.0237-0.0442-0.0064-0.022715.012-3.20497.348
74.50910.72744.80591.88470.310313.1034-0.07750.2258-0.18870.05120.0305-0.18580.09550.23240.0469-0.12690.0618-0.0173-0.04890.0078-0.00044.799.82663.598
86.96742.1924.435913.287116.567831.83930.2771.3283-0.70050.10030.9719-0.57140.65912.206-1.2489-0.13480.1807-0.06830.2263-0.13150.090414.6347.39165.188
914.842-5.0404-5.139410.03754.399813.80.51970.7652-0.0067-0.4367-0.0758-0.6807-0.65660.237-0.444-0.04710.0624-0.0056-0.00720.01040.058810.69318.75863.448
105.3052-1.22271.45451.6849-1.08383.154-0.0771-0.08360.30420.0785-0.1065-0.2301-0.3132-0.01660.1835-0.08150.06420.0026-0.0713-0.00010.01411.92617.90375.036
114.71043.79371.098310.23137.875112.48530.035-0.30920.06260.2189-0.32390.44010.2887-1.47160.2889-0.17390.05680.01450.17-0.0056-0.0199-5.51812.16667.62
128.2463-3.51041.86824.14575.695524.0870.5634-0.3288-0.66210.05630.0360.11012.165-0.4632-0.59940.099-0.1059-0.1005-0.05730.0383-0.018-3.7562.44548.102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 28
2X-RAY DIFFRACTION2A29 - 39
3X-RAY DIFFRACTION3A40 - 50
4X-RAY DIFFRACTION4A51 - 61
5X-RAY DIFFRACTION5A62 - 75
6X-RAY DIFFRACTION6A76 - 111
7X-RAY DIFFRACTION7B8 - 27
8X-RAY DIFFRACTION8B28 - 44
9X-RAY DIFFRACTION9B45 - 58
10X-RAY DIFFRACTION10B59 - 81
11X-RAY DIFFRACTION11B82 - 93
12X-RAY DIFFRACTION12B94 - 111

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