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- PDB-2q2k: Structure of nucleic-acid binding protein -

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Basic information

Entry
Database: PDB / ID: 2q2k
TitleStructure of nucleic-acid binding protein
Components
  • DNA (5'-D(*AP*GP*TP*AP*TP*AP*(5IU)P*AP*CP*(5IU)P*AP*GP*TP*AP*TP*AP*TP*AP*CP*T)-3')
  • Hypothetical protein
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA / partition / segregation / parB / DNA BINDING PROTEIN-DNA COMPLEX
Function / homologyArc Repressor Mutant - #20 / Arc Repressor Mutant / Helix non-globular / Special / DNA / DNA (> 10) / Conserved domain protein / Uncharacterized protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsSchumacher, M.A. / Glover, T. / Firth, N.
CitationJournal: Nature / Year: 2007
Title: Segrosome structure revealed by a complex of ParR with centromere DNA.
Authors: Schumacher, M.A. / Glover, T.C. / Brzoska, A.J. / Jensen, S.O. / Dunham, T.D. / Skurray, R.A. / Firth, N.
History
DepositionMay 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
F: DNA (5'-D(*AP*GP*TP*AP*TP*AP*(5IU)P*AP*CP*(5IU)P*AP*GP*TP*AP*TP*AP*TP*AP*CP*T)-3')
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9284
Polymers22,6893
Non-polymers2381
Water00
1
F: DNA (5'-D(*AP*GP*TP*AP*TP*AP*(5IU)P*AP*CP*(5IU)P*AP*GP*TP*AP*TP*AP*TP*AP*CP*T)-3')
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

F: DNA (5'-D(*AP*GP*TP*AP*TP*AP*(5IU)P*AP*CP*(5IU)P*AP*GP*TP*AP*TP*AP*TP*AP*CP*T)-3')
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8558
Polymers45,3796
Non-polymers4772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)56.300, 56.300, 232.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 6354.755 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Hypothetical protein


Mass: 8167.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2FDA3, UniProt: O87365*PLUS
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

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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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2isopropanol11
3HEPES11
4PEG 400012
5isopropanol12
6HEPES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2007 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3→77.6 Å / Num. all: 4650 / Num. obs: 4506 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 87 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 3→3.19 Å / Redundancy: 3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.1 / Num. unique all: 450 / Rsym value: 0.365 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 3→41.27 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1236191.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 426 9.5 %RANDOM
Rwork0.258 ---
obs0.258 4506 91.7 %-
all-4650 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0649 Å2 / ksol: 0.342795 e/Å3
Displacement parametersBiso mean: 77.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.22 Å221.74 Å20 Å2
2--8.22 Å20 Å2
3----16.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 407 15 0 1184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d1.29
X-RAY DIFFRACTIONc_mcbond_it2.631.5
X-RAY DIFFRACTIONc_mcangle_it4.472
X-RAY DIFFRACTIONc_scbond_it3.662
X-RAY DIFFRACTIONc_scangle_it5.692.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 49 9.1 %
Rwork0.423 492 -
obs-450 69.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna.param.txtdna-rna.top
X-RAY DIFFRACTION5hepes.paramhepes.top

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