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- PDB-4egy: Crystal Structure of AraR(DBD) in complex with operator ORA1 -

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Basic information

Entry
Database: PDB / ID: 4egy
TitleCrystal Structure of AraR(DBD) in complex with operator ORA1
Components
  • 5'-D(*AP*AP*AP*AP*TP*TP*GP*TP*TP*CP*GP*TP*AP*CP*AP*AP*AP*TP*AP*TP*T)-3'
  • 5'-D(*TP*AP*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*AP*AP*CP*AP*AP*TP*TP*T)-3'
  • Arabinose metabolism transcriptional repressor
KeywordsTRANSCRIPTION/DNA / winged helix turn helix / transcription factor / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Arabinose metabolism transcriptional repressor, ligand-binding domain / Transcriptional regulator LacI/GalR-like, sensor domain / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Periplasmic binding protein-like domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Periplasmic binding protein-like I / Arc Repressor Mutant, subunit A ...Arabinose metabolism transcriptional repressor, ligand-binding domain / Transcriptional regulator LacI/GalR-like, sensor domain / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Periplasmic binding protein-like domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Periplasmic binding protein-like I / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Arabinose metabolism transcriptional repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsJain, D. / Nair, D.T.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators.
Authors: Jain, D. / Nair, D.T.
History
DepositionApr 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Other
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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.value / _struct_conn.pdbx_dist_value / _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.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_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: Arabinose metabolism transcriptional repressor
B: Arabinose metabolism transcriptional repressor
T: 5'-D(*TP*AP*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*AP*AP*CP*AP*AP*TP*TP*T)-3'
U: 5'-D(*AP*AP*AP*AP*TP*TP*GP*TP*TP*CP*GP*TP*AP*CP*AP*AP*AP*TP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9598
Polymers32,7424
Non-polymers2174
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-39 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.730, 42.520, 67.580
Angle α, β, γ (deg.)90.00, 114.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Arabinose metabolism transcriptional repressor


Mass: 9931.353 Da / Num. of mol.: 2 / Fragment: N-terminal Domain, UNP RESIDUES 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: araC, araR, BSU33970, yvbS / Plasmid: pDJN1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: P96711

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DNA chain , 2 types, 2 molecules TU

#2: DNA chain 5'-D(*TP*AP*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*AP*AP*CP*AP*AP*TP*TP*T)-3'


Mass: 6435.208 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*AP*AP*AP*TP*TP*GP*TP*TP*CP*GP*TP*AP*CP*AP*AP*AP*TP*AP*TP*T)-3'


Mass: 6444.222 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 105 molecules

#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 26% PEG 8000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0072refinement
CNS1.2refinement
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.301→35.959 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 30.2 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2623 953 6.02 %
Rwork0.2222 --
obs0.2247 15834 96.73 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.121 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.79 Å2-0 Å215.3169 Å2
2---9.6515 Å20 Å2
3----8.1385 Å2
Refinement stepCycle: LAST / Resolution: 2.301→35.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 855 13 101 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072169
X-RAY DIFFRACTIONf_angle_d1.2723104
X-RAY DIFFRACTIONf_dihedral_angle_d24.522863
X-RAY DIFFRACTIONf_chiral_restr0.061345
X-RAY DIFFRACTIONf_plane_restr0.006255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3011-2.42240.38421480.34822094X-RAY DIFFRACTION96
2.4224-2.57410.36021320.28112100X-RAY DIFFRACTION97
2.5741-2.77280.3571310.25062121X-RAY DIFFRACTION97
2.7728-3.05170.28991580.25182113X-RAY DIFFRACTION97
3.0517-3.4930.24161000.22292118X-RAY DIFFRACTION96
3.493-4.39950.2191410.19432133X-RAY DIFFRACTION97
4.3995-35.96330.23721430.19412202X-RAY DIFFRACTION97
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)
10.18420.02550.1190.409-0.0220.08240.112-0.1201-0.10050.2248-0.03130.00650.0342-0.0711-0.10540.5264-0.10180.04520.1930.06050.626612.266837.797113.4281
20.44090.431-0.23060.4292-0.24970.86340.2770.050.02140.0099-0.15050.1936-0.25810.01-0.00270.20030.0372-0.02040.20840.0290.340614.230229.1516-2.5563
30.46480.17490.15290.15340.08350.1306-0.1361-0.10940.4505-0.0823-0.1099-0.03850.0960.04230.050.483-0.02870.06530.26230.01750.466416.89110.9324-3.882
40.3416-0.06070.00480.198-0.16630.14740.03770.2383-0.41590.1487-0.0186-0.10450.4261-0.13060.01610.5181-0.1324-0.06930.23760.0070.3239.73083.95346.4562
50.03570.04220.02210.3921-0.01560.0202-0.04880.0187-0.1930.21530.05780.08320.07550.0020.09140.2721-0.11310.02240.31530.01310.51350.07574.186515.2045
60.4104-0.099-0.10960.3349-0.33670.4480.1641-0.1731-0.24210.03230.12030.04680.2709-0.0205-0.03360.38710.0394-0.07320.19270.05960.219715.67715.675216.431
71.4310.12890.27550.1829-0.18590.43960.2284-0.4433-0.03240.0109-0.3836-0.12410.0716-0.03330.15490.1993-0.011-0.0260.27110.00150.376511.440913.50469.3811
80.1480.05650.0340.13220.12540.1302-0.0484-0.12310.0506-0.0334-0.09210.1427-0.07250.0263-0.00570.1155-0.053-0.05520.3-0.08310.30051.888113.833314.9209
90.7512-0.33480.671.11810.31820.99040.04690.07680.06720.02540.4335-0.06720.24030.13540.30920.54490.01410.30260.3608-0.05090.41339.708921.017638.982
101.105-0.0667-0.42440.5083-0.3060.3805-0.2191-0.2317-0.01020.685-0.30720.28560.1599-0.04710.09340.4443-0.08990.02920.2945-0.03430.182612.277117.947221.373
110.75970.8359-0.71931.5701-0.78060.7177-0.03540.22040.2909-0.16810.29090.0142-0.3450.17820.19570.3121-0.10120.18970.3581-0.26710.292226.542422.22269.6448
121.2140.2532-0.61980.6590.32470.65820.19160.09130.2805-0.30290.4905-0.04760.09280.3345-0.22740.40490.0338-0.07350.25230.01970.218926.504714.5186-8.4829
130.488-0.2486-0.11440.63740.29750.22370.17470.20170.0646-0.19790.08850.0373-0.25590.1299-0.11750.28870.02260.01050.3056-0.02620.182127.366217.529-5.2415
140.35820.3576-0.59251.922-0.24173.22020.1995-0.23410.17740.41990.31530.54530.8430.19260.59050.58060.00350.17510.2078-0.04040.221214.427919.596525.266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A' AND (RESSEQ -12:3)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 4:68)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ -1:3)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 4:15)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 16:29)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 30:40)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 41:53)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 54:68)
9X-RAY DIFFRACTION9CHAIN T AND (RESSEQ 1:5)
10X-RAY DIFFRACTION10CHAIN T AND (RESSEQ 6:10)
11X-RAY DIFFRACTION11CHAIN T AND (RESSEQ 11:15)
12X-RAY DIFFRACTION12CHAIN T AND (RESSEQ 16:21)
13X-RAY DIFFRACTION13CHAIN U AND (RESSEQ 22:31)
14X-RAY DIFFRACTION14CHAIN U AND (RESSEQ 32:42)

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