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- PDB-1p71: Anabaena HU-DNA corcrystal structure (TR3) -

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Basic information

Entry
Database: PDB / ID: 1p71
TitleAnabaena HU-DNA corcrystal structure (TR3)
Components
  • 5'-D(*TP*GP*CP*TP*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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'
D: 5'-D(*TP*GP*CP*TP*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)32,9374
Polymers32,9374
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.441, 93.062, 100.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'


Mass: 6379.131 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.: 196 / 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: 2.61 Å3/Da / Density % sol: 52.45 %
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
8odium azide11
9H2O11
10Peg 500012
11glycerol12
12potassium chlorid12
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: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2001
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 20602 / Num. obs: 20602 / % possible obs: 72.4 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.041
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.3 / % possible all: 20.9
Reflection
*PLUS
Lowest resolution: 100 Å / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8Z with nonidentical sidechains pruned back to a common atom

1b8z


Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.985 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.224
Details: Data are anisotropic with limits 1.9 X 2.5 x 2.0. Data were truncated to an ellipsoid and reflections with an average (I/sigI) ratio less than 2 were removed. The completeness above is ...Details: Data are anisotropic with limits 1.9 X 2.5 x 2.0. Data were truncated to an ellipsoid and reflections with an average (I/sigI) ratio less than 2 were removed. The completeness above is underestimated. When truncation is factored in, data in refinement are 91% complete. The following residues in chain A and B have some sidechain atoms with 0.00 occupancy: A3, A12, A13, A18, A19, A34, A45, A59, B3, B12, B18, B59, B67, B83, B84.
RfactorNum. reflection% reflectionSelection details
Rfree0.28788 941 4.8 %RANDOM
Rwork0.24415 ---
obs0.24637 18562 68.62 %-
all-28420 --
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: 31.952 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--5.48 Å20 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 791 0 196 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212255
X-RAY DIFFRACTIONr_angle_refined_deg1.7452.4063208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195185
X-RAY DIFFRACTIONr_chiral_restr0.0870.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021411
X-RAY DIFFRACTIONr_nbd_refined0.2220.2904
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.213
X-RAY DIFFRACTIONr_mcbond_it0.4831.5932
X-RAY DIFFRACTIONr_mcangle_it0.89621483
X-RAY DIFFRACTIONr_scbond_it1.72531323
X-RAY DIFFRACTIONr_scangle_it2.7324.51725
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.217 19
Rwork0.293 401
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)
16.33120.2406-0.2922.7825-0.21284.7185-0.0765-1.156-0.17180.2933-0.0357-0.04980.1270.06470.11220.04430.06770.00930.3970.09370.111918.787915.777787.9444
21.4165-3.24310.83477.7895-6.17358.90280.1165-0.07550.1032-0.0865-0.4459-0.0616-0.49460.55980.32940.094-0.0058-0.04770.1147-0.00810.129831.742228.832464.7368
32.2568-2.4381-1.46863.95753.57611.136-0.06090.0422-0.0731-0.3550.1086-0.09110.109-0.4437-0.04770.0708-0.06890.0370.08660.01270.14076.469213.572562.3901
41.93113.75490.8246.9071.70331.52560.2673-0.4445-0.03060.4449-0.29270.05180.3689-0.15410.02540.3718-0.0653-0.01380.0556-0.02630.270818.882821.348963.82
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC1 - 521 - 52
2X-RAY DIFFRACTION1BD1 - 521 - 52
3X-RAY DIFFRACTION1AC77 - 9477 - 94
4X-RAY DIFFRACTION1BD77 - 9377 - 93
5X-RAY DIFFRACTION2AC53 - 7653 - 76
6X-RAY DIFFRACTION3BD53 - 7653 - 76
7X-RAY DIFFRACTION4CA1 - 201 - 20
8X-RAY DIFFRACTION4DB1 - 201 - 20
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.745

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