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- PDB-4cj9: BurrH DNA-binding protein from Burkholderia rhizoxinica in its ap... -

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Basic information

Entry
Database: PDB / ID: 4cj9
TitleBurrH DNA-binding protein from Burkholderia rhizoxinica in its apo form
ComponentsBURRH
KeywordsTRANSCRIPTION / GENE TARGETING / PROTEIN-DNA INTERACTION
Function / homologyAnkyrin repeat region circular profile. / Ankyrin repeat-containing domain superfamily / double-stranded DNA binding / SELENIUM ATOM / Burkholderia TALE-like protein 1
Function and homology information
Biological speciesBURKHOLDERIA RHIZOXINICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.214 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 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: BURRH
B: BURRH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,1924
Polymers167,0342
Non-polymers1582
Water16,358908
1
A: BURRH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6753
Polymers83,5171
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BURRH


Theoretical massNumber of molelcules
Total (without water)83,5171
Polymers83,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.314, 73.314, 268.337
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein BURRH


Mass: 83517.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA RHIZOXINICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E5AV36*PLUS
#2: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97974
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97974 Å / Relative weight: 1
ReflectionResolution: 2.21→46.08 Å / Num. obs: 79217 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 39.02 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.214→63.492 Å / SU ML: 0.25 / σ(F): 0.27 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1981 2.5 %
Rwork0.1797 --
obs0.181 79112 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.214→63.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10954 0 2 908 11864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311086
X-RAY DIFFRACTIONf_angle_d0.71214949
X-RAY DIFFRACTIONf_dihedral_angle_d13.8054091
X-RAY DIFFRACTIONf_chiral_restr0.0451722
X-RAY DIFFRACTIONf_plane_restr0.0042017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2144-2.26980.32251340.23195483X-RAY DIFFRACTION98
2.2698-2.33120.2821320.21515418X-RAY DIFFRACTION98
2.3312-2.39980.24291430.20325609X-RAY DIFFRACTION99
2.3998-2.47720.31241360.21165478X-RAY DIFFRACTION99
2.4772-2.56580.29141470.20865556X-RAY DIFFRACTION99
2.5658-2.66850.29581440.20565578X-RAY DIFFRACTION99
2.6685-2.790.25161420.19385544X-RAY DIFFRACTION100
2.79-2.9370.24371430.18555691X-RAY DIFFRACTION100
2.937-3.12110.24541420.19535504X-RAY DIFFRACTION100
3.1211-3.3620.27311430.18965610X-RAY DIFFRACTION100
3.362-3.70030.21651380.17285574X-RAY DIFFRACTION100
3.7003-4.23570.20491460.15725601X-RAY DIFFRACTION100
4.2357-5.33610.19381440.15955593X-RAY DIFFRACTION100
5.3361-63.51790.18811470.17055592X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.7557 Å / Origin y: 36.4997 Å / Origin z: 132.5729 Å
111213212223313233
T0.3206 Å2-0.0203 Å2-0.0156 Å2-0.2384 Å20.0038 Å2--0.3011 Å2
L0.1032 °2-0.0372 °2-0.0271 °2-0.0298 °2-0.0744 °2--0.5783 °2
S0.0351 Å °-0.0221 Å °-0.0284 Å °0.0172 Å °-0.0009 Å °0.0025 Å °0.0171 Å °0.0459 Å °-0.0351 Å °
Refinement TLS groupSelection details: ALL

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