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- PDB-1r71: Crystal Structure of the DNA binding domain of KorB in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1r71
TitleCrystal Structure of the DNA binding domain of KorB in complex with the operator DNA
Components
  • 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
  • 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
  • Transcriptional repressor protein korB
KeywordsTRANSCRIPTION/DNA / IncP / plasmid partitioning / protein-DNA complex / heilx-turn-helix motif / transcription factor / ParB homologue / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of DNA-templated transcription / protein-containing complex / DNA binding / identical protein binding
Similarity search - Function
KorB DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #140 / KorB, C-terminal / Repressor KorB domain / KorB, C-terminal domain superfamily / KorB DNA-binding domain / KorB C-terminal beta-barrel domain / KorB domain / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain ...KorB DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #140 / KorB, C-terminal / Repressor KorB domain / KorB, C-terminal domain superfamily / KorB DNA-binding domain / KorB C-terminal beta-barrel domain / KorB domain / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Transcriptional repressor, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional repressor protein KorB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKhare, D. / Ziegelin, G. / Lanka, E. / Heinemann, U.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB.
Authors: Khare, D. / Ziegelin, G. / Lanka, E. / Heinemann, U.
History
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
I: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
F: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
J: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
G: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
L: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
H: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
K: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
A: Transcriptional repressor protein korB
B: Transcriptional repressor protein korB
C: Transcriptional repressor protein korB
D: Transcriptional repressor protein korB


Theoretical massNumber of molelcules
Total (without water)122,22512
Polymers122,22512
Non-polymers00
Water6,251347
1
E: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
I: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
F: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
J: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
A: Transcriptional repressor protein korB
B: Transcriptional repressor protein korB


Theoretical massNumber of molelcules
Total (without water)61,1136
Polymers61,1136
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
L: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
H: 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'
K: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'
C: Transcriptional repressor protein korB
D: Transcriptional repressor protein korB


Theoretical massNumber of molelcules
Total (without water)61,1136
Polymers61,1136
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.440, 110.440, 160.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly comprises of two protein molecules (chain A and B) bound to a DNA duplex (chain E and F)

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Components

#1: DNA chain
5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'


Mass: 5315.305 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'


Mass: 5291.113 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
Transcriptional repressor protein korB


Mass: 19949.949 Da / Num. of mol.: 4 / Fragment: Operator Binding Domain (residues 117-294)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: KORB / Plasmid: pMS51-12 / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1, supE44, relA1 / References: UniProt: P07674
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 25% MPD, 0.4M ammonium dihydrogen phosphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2ammonium dihydrogen phosphate11
3H2O11
4MPD12
5H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92022, 0.92039, 0.89844
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 2003 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.920221
20.920391
30.898441
ReflectionResolution: 2.2→30 Å / Num. all: 57947 / Num. obs: 57669 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.077 / Net I/σ(I): 14.91
Reflection shellResolution: 2.2→2.24 Å / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.591 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The DNA in the co-crystal has dual occupancy in the two complexes. There are certain water molecules showing close contact to one of the ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The DNA in the co-crystal has dual occupancy in the two complexes. There are certain water molecules showing close contact to one of the strand. These water molecules form hydrogen bonds to the other overlaying stand and therefore are kept at occupancy 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.25028 2911 5 %RANDOM
Rwork0.19481 ---
obs0.19759 54758 99.51 %-
all-57947 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.497 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å2-0.73 Å20 Å2
2---1.47 Å20 Å2
3---2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 2764 0 347 6769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216799
X-RAY DIFFRACTIONr_bond_other_d0.0020.024808
X-RAY DIFFRACTIONr_angle_refined_deg2.0122.4729760
X-RAY DIFFRACTIONr_angle_other_deg0.949311440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8035453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025559
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02761
X-RAY DIFFRACTIONr_nbd_refined0.2380.21074
X-RAY DIFFRACTIONr_nbd_other0.2440.24593
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.22327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2331
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0530.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.822273
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2533688
X-RAY DIFFRACTIONr_scbond_it3.7314.54526
X-RAY DIFFRACTIONr_scangle_it4.97466072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.278 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.312 272
Rwork0.253 5118

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