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- PDB-2o97: Crystal Structure of E. coli HU heterodimer -

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Basic information

Entry
Database: PDB / ID: 2o97
TitleCrystal Structure of E. coli HU heterodimer
Components
  • DNA-binding protein HU-alpha
  • DNA-binding protein HU-beta
KeywordsDNA BINDING PROTEIN / DNA-binding / heterodimer / DNA structure / DNA supercoiling / E. coli
Function / homology
Function and homology information


HU-DNA complex / DnaA-HU complex / bacterial nucleoid DNA packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding ...HU-DNA complex / DnaA-HU complex / bacterial nucleoid DNA packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding / identical protein binding / membrane / 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
NICKEL (II) ION / DNA-binding protein HU-alpha / DNA-binding protein HU-beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGuo, F. / Adhya, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Spiral structure of Escherichia coli HU{alpha}beta provides foundation for DNA supercoiling.
Authors: Guo, F. / Adhya, S.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8844
Polymers18,7902
Non-polymers942
Water46826
1
A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-beta
hetero molecules

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-beta
hetero molecules

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-beta
hetero molecules

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,53516
Polymers75,1588
Non-polymers3778
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x+1/2,z+1/41
crystal symmetry operation6_675-x+1,-y+2,z1
crystal symmetry operation8_565y,-x+3/2,z+1/41
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-52 kcal/mol
Surface area7350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.915, 82.915, 61.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsFour dimers form a tetragonal unit of a spiral filament by symmetry operation. The space group is I41.

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Components

#1: Protein DNA-binding protein HU-alpha / NS2 / HU-2


Mass: 9549.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupA / Plasmid: pRLM118 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF0
#2: Protein DNA-binding protein HU-beta / NS1 / HU-1


Mass: 9239.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupB, hopD / Plasmid: pRLM118 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 0.1M Tris-HCl, 0.01M nickel chloride, 20% PEG-MME2000, 5% glycerol, pH 8.5, EVAPORATION, temperature 298K, pH 8.50

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 7084 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 6.23 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 28.3
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.362 / % possible all: 64.7

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Phasing

Phasing MRRfactor: 0.526 / Cor.coef. Fo:Fc: 0.643
Highest resolutionLowest resolution
Rotation2.6 Å31.67 Å
Translation2.6 Å31.67 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 4583
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.85-100400.709508
4.66-5.8548.30.788504
4.08-4.6640.20.867503
3.72-4.0843.90.837501
3.45-3.7247.70.818501
3.26-3.4550.80.839502
3.09-3.2650.20.829502
2.95-3.0953.50.761505
2.79-2.9546.40.822557

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM4.2phasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 26.752 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 361 5.1 %RANDOM
Rwork0.226 ---
obs0.228 7084 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å20 Å2
2---2.25 Å20 Å2
3---4.5 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 2 26 1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221032
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9761380
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12526.38936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.89915195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.137153
X-RAY DIFFRACTIONr_chiral_restr0.0880.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02719
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.2517
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2692
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6751.5720
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12821090
X-RAY DIFFRACTIONr_scbond_it1.843354
X-RAY DIFFRACTIONr_scangle_it2.9244.5290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 27 -
Rwork0.314 339 -
obs--68.67 %
Refinement TLS params.Method: refined / Origin x: 41.6916 Å / Origin y: 61.3725 Å / Origin z: -1.4093 Å
111213212223313233
T-0.1073 Å20.0412 Å2-0.0634 Å2-0.1735 Å2-0.2416 Å2--0.111 Å2
L3.379 °2-0.0984 °2-0.521 °2-7.6291 °21.0204 °2--3.6506 °2
S-0.0613 Å °-0.5422 Å °0.4606 Å °0.1688 Å °0.0167 Å °0.1923 Å °-0.0528 Å °-0.0166 Å °0.0446 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 901 - 90
2X-RAY DIFFRACTION1BB1 - 901 - 90

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