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- PDB-4h0e: Crystal Structure of mutant ORR3 in complex with NTD of AraR -

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Basic information

Entry
Database: PDB / ID: 4h0e
TitleCrystal Structure of mutant ORR3 in complex with NTD of AraR
Components
  • 5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*CP*AP*TP*TP*TP*TP*AP*T)-3'
  • 5'-D(*TP*AP*TP*AP*AP*AP*AP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'
  • Arabinose metabolism transcriptional repressor
KeywordsTRANSCRIPTION/DNA / WINGED HELIX TURN HELIX / TRANSCRIPTION FACTOR / DNA / 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: 1.973 Å
AuthorsNair, D.T. / Jain, D.
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
DepositionSep 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
U: 5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*CP*AP*TP*TP*TP*TP*AP*T)-3'
T: 5'-D(*TP*AP*TP*AP*AP*AP*AP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9608
Polymers32,7434
Non-polymers2174
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-37 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.800, 42.620, 67.440
Angle α, β, γ (deg.)90.00, 114.92, 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-terminus 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 UT

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


Mass: 6402.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: YES
#3: DNA chain 5'-D(*TP*AP*TP*AP*AP*AP*AP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*AP*AP*TP*T)-3'


Mass: 6478.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: YES

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Non-polymers , 3 types, 160 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.: 156 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.2
Details: 25% PEG 8000, pH 4.2, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2012
RadiationMonochromator: Bartels / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.973→40.339 Å / Num. all: 25314 / Num. obs: 24656 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.973→2.08 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PXIIIprogramdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EGZ

4egz


Resolution: 1.973→40.339 Å / SU ML: 0.23 / σ(F): 0 / σ(I): 0 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1212 5.07 %RANDOM
Rwork0.2192 ---
all0.2209 24593 --
obs0.2209 23894 94.23 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.075 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.9461 Å20 Å210.2573 Å2
2---6.0025 Å2-0 Å2
3----4.9437 Å2
Refinement stepCycle: LAST / Resolution: 1.973→40.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 855 13 156 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132257
X-RAY DIFFRACTIONf_angle_d1.3453100
X-RAY DIFFRACTIONf_dihedral_angle_d23.95860
X-RAY DIFFRACTIONf_chiral_restr0.063344
X-RAY DIFFRACTIONf_plane_restr0.005255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.973-2.0520.29271280.2421234287
2.052-2.14540.27871190.2261237191
2.1454-2.25850.2871460.2222245392
2.2585-2.40.26441240.23247093
2.4-2.58520.31051390.241253896
2.5852-2.84530.31611520.2427258097
2.8453-3.25690.28171290.2401258897
3.2569-4.10270.2051360.2032261298
4.1027-40.34710.22071390.2021272898

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