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- PDB-1p78: Anabaena HU-DNA cocrystal structure (AHU2) -

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Basic information

Entry
Database: PDB / ID: 1p78
TitleAnabaena HU-DNA cocrystal structure (AHU2)
Components
  • 5'-D(*TP*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'
  • DNA-binding protein HU
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / DNA bending / HU / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


heterocyst development / chromosome condensation / structural constituent of chromatin / DNA binding / cytosol
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein HU
Similarity search - Component
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsSwinger, K.S. / Lemberg, K.M. / Zhang, Y. / Rice, P.A.
CitationJournal: Embo J. / Year: 2003
Title: Flexible DNA bending in HU-DNA cocrystal structures
Authors: Swinger, K.S. / Lemberg, K.M. / Zhang, Y. / Rice, P.A.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*TP*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'
D: 5'-D(*TP*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'
A: DNA-binding protein HU
B: DNA-binding protein HU


Theoretical massNumber of molelcules
Total (without water)32,9554
Polymers32,9554
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.430, 91.810, 100.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTHRTHRAC7 - 177 - 17
21VALVALTHRTHRBD7 - 177 - 17
32GLNGLNGLUGLUAC20 - 3420 - 34
42GLNGLNGLUGLUBD20 - 3420 - 34
DetailsThe assymetric unit contains one functional complex composed of a protein homodimer and duplex DNA.

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Components

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


Mass: 6388.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized DNA
#2: Protein DNA-binding protein HU


Mass: 10089.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Gene: HUP OR HANA OR ASR3935 / Plasmid: pET21A (pETAHU) / Production host: Escherichia coli (E. coli) / Strain (production host): RJ1878 lacks functional HU genes / References: UniProt: P05514
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.7 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peg 5000 monomethyl ether, glycerol, tris, jeffamine, potassium chloride, calcium chloride, sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1Peg 500011
2monomethyl ether11
3glycerol11
4tris11
5jeffamine11
6potassium chloride11
7calcium chloride11
8sodium azide11
9H2O11
10Peg 500012
11glycerol12
12potassium chloride12
13calcium chloride12
14sodium azide12
15H2O12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1reservoirKCl
210 %glycerol1reservoir
350 mMTris1reservoirpH7.5 or pH8.0
40.02 %1reservoirNaN3
51 %Jaffamine1reservoirpH7.0
612-22.5 %PEG5000 MME1reservoir
720 mM1reservoirCaCl2
81
91
101
111
121
131
141
151

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0078 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 14, 2002
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0078 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 16454 / Num. obs: 16454 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.376 / % possible all: 54.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1P71

1p71


Resolution: 2.25→25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.913 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: restrained invidual isotropic (after TLS refinement)
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.269 / Stereochemistry target values: Refmac 5.1.24 library
RfactorNum. reflection% reflectionSelection details
Rfree0.27589 677 4.6 %RANDOM
Rwork0.23908 ---
obs0.24089 13935 85.16 %-
all-17158 --
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: 25.498 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--2.99 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 812 0 94 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6252.4153269
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7485182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021434
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2950
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0240.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4211.5915
X-RAY DIFFRACTIONr_mcangle_it0.78721467
X-RAY DIFFRACTIONr_scbond_it1.68831386
X-RAY DIFFRACTIONr_scangle_it2.554.51802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 183 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.140.5
medium thermal0.382
LS refinement shellResolution: 2.25→2.371 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.411 47
Rwork0.336 1235
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.44020.12570.08373.21190.2044.3348-0.1221-1.121-0.17110.53650.0179-0.08080.16690.11380.10420.18680.08030.01280.51750.080.211319.21415.237188.7704
22.3716-2.0081-0.6657.1912-3.7776.66720.1143-0.06420.089-0.3651-0.2105-0.1928-0.17820.34050.09630.0604-0.0311-0.06470.1519-0.0130.115132.04828.304564.8618
32.5142-2.5451-0.64794.28053.983410.8624-0.1048-0.0151-0.0653-0.20070.15310.0621-0.0778-0.0547-0.04830.1032-0.01190.01380.14470.03150.1026.616913.391562.2819
44.5763-1.4454-2.65998.72320.28578.6714-0.0145-0.39760.59620.8406-0.00620.48250.2479-0.89860.02060.281-0.0360.04190.2367-0.18010.241422.0341.097870.8414
54.35191.94390.59275.6616-0.3558-0.9205-0.098-0.1792-0.3681-0.1545-0.2495-0.80970.1948-0.06550.34750.2579-0.0450.00090.0711-0.05250.131220.617121.250760.8879
67.2716-4.01586.99269.7416-3.96320.76960.266-0.4629-1.1317-0.1767-0.1019-0.02391.46580.9843-0.1640.6124-0.0246-0.01260.26160.18750.330214.5611-1.329464.0045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION1B1 - 52
3X-RAY DIFFRACTION1A77 - 92
4X-RAY DIFFRACTION1B77 - 92
5X-RAY DIFFRACTION2A53 - 76
6X-RAY DIFFRACTION3B53 - 76
7X-RAY DIFFRACTION4C1 - 5
8X-RAY DIFFRACTION4D16 - 20
9X-RAY DIFFRACTION5C6 - 15
10X-RAY DIFFRACTION5D5 - 15
11X-RAY DIFFRACTION6C16 - 20
12X-RAY DIFFRACTION6D1 - 4
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.625

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