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- PDB-4cja: BurrH DNA-binding protein from Burkholderia rhizoxinica in comple... -

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Basic information

Entry
Database: PDB / ID: 4cja
TitleBurrH DNA-binding protein from Burkholderia rhizoxinica in complex with its target DNA
Components
  • 5'-D(*DTP*AP*TP*AP*AP*CP*GP*TP*AP*TP*TP*TP*GP*CP *TP*TP*CP*TP*CP*TP*TP*AP*AP)-3'
  • 5'-D(*DTP*TP*AP*AP*GP*AP*GP*AP*AP*GP*CP*AP*AP*DP *TP*AP*CP*GP*TP*TP*AP*TP*AP)-3'
  • BURRH
KeywordsTRANSCRIPTION / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesBURKHOLDERIA RHIZOXINICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsStella, S. / Molina, R. / Lopez-Mendez, B. / Campos-Olivas, R. / Duchateau, P. / Montoya, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Bud, a Helix-Loop-Helix DNA-Binding Domain for Genome Modification
Authors: Stella, S. / Molina, R. / Lopez-Mendez, B. / Juillerat, A. / Bertonati, C. / Daboussi, F. / Campos-Olivas, R. / Duchateau, P. / Montoya, G.
History
DepositionDec 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BURRH
B: 5'-D(*DTP*TP*AP*AP*GP*AP*GP*AP*AP*GP*CP*AP*AP*DP *TP*AP*CP*GP*TP*TP*AP*TP*AP)-3'
C: 5'-D(*DTP*AP*TP*AP*AP*CP*GP*TP*AP*TP*TP*TP*GP*CP *TP*TP*CP*TP*CP*TP*TP*AP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)97,0713
Polymers97,0713
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-98.1 kcal/mol
Surface area35150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.242, 95.950, 76.446
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BURRH


Mass: 82954.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA RHIZOXINICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
#2: DNA chain 5'-D(*DTP*TP*AP*AP*GP*AP*GP*AP*AP*GP*CP*AP*AP*DP *TP*AP*CP*GP*TP*TP*AP*TP*AP)-3'


Mass: 7120.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BURKHOLDERIA RHIZOXINICA (bacteria)
#3: DNA chain 5'-D(*DTP*AP*TP*AP*AP*CP*GP*TP*AP*TP*TP*TP*GP*CP *TP*TP*CP*TP*CP*TP*TP*AP*AP)-3'


Mass: 6995.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BURKHOLDERIA RHIZOXINICA (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→47.92 Å / Num. obs: 27134 / % possible obs: 97.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 65.54 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.651→38.656 Å / SU ML: 0.41 / σ(F): 1.45 / Phase error: 34.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 1392 5 %
Rwork0.2027 --
obs0.2063 27077 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.651→38.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 937 0 125 6553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086598
X-RAY DIFFRACTIONf_angle_d1.3669097
X-RAY DIFFRACTIONf_dihedral_angle_d21.7692498
X-RAY DIFFRACTIONf_chiral_restr0.0821045
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6514-2.74620.33891280.25162602X-RAY DIFFRACTION99
2.7462-2.85610.3161470.24482627X-RAY DIFFRACTION100
2.8561-2.9860.35141190.2482622X-RAY DIFFRACTION100
2.986-3.14340.37191430.26422654X-RAY DIFFRACTION100
3.1434-3.34020.33691340.23812613X-RAY DIFFRACTION99
3.3402-3.5980.35361170.23182633X-RAY DIFFRACTION99
3.598-3.95970.30821320.21122654X-RAY DIFFRACTION100
3.9597-4.53190.2381560.17572626X-RAY DIFFRACTION100
4.5319-5.70680.24911500.1812633X-RAY DIFFRACTION100
5.7068-38.66060.20861660.17652663X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 30.7165 Å / Origin y: 55.4354 Å / Origin z: 56.5632 Å
111213212223313233
T0.3316 Å2-0.0043 Å20.0346 Å2-0.2804 Å20.0704 Å2--0.4567 Å2
L1.1025 °2-0.4478 °2-1.0238 °2-1.056 °20.9836 °2--2.6075 °2
S-0.0808 Å °-0.1173 Å °-0.0893 Å °0.2694 Å °0.0145 Å °0.1886 Å °0.2021 Å °-0.0854 Å °0.0557 Å °
Refinement TLS groupSelection details: ALL

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