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- PDB-4yfh: HU38-20bp -

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Basic information

Entry
Database: PDB / ID: 4yfh
TitleHU38-20bp
Components
  • (synthetic DNA strand) x 2
  • DNA-binding protein HU-alpha
KeywordsDNA BINDING PROTEIN/DNA / HU-DNA / transcription / pathogenicity / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


HU-DNA complex / DnaA-HU complex / bacterial nucleoid 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 packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding / membrane / identical protein 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-alpha / DNA-binding protein HU-alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.49 Å
AuthorsHammel, M. / Reyes, F.E. / Parpana, R. / Tainer, J.A. / Adhya, S. / Amlanjyoti, D.
CitationJournal: Sci Adv / Year: 2016
Title: HU multimerization shift controls nucleoid compaction.
Authors: Hammel, M. / Amlanjyoti, D. / Reyes, F.E. / Chen, J.H. / Parpana, R. / Tang, H.Y. / Larabell, C.A. / Tainer, J.A. / Adhya, S.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 27, 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
A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha
C: synthetic DNA strand
D: synthetic DNA strand


Theoretical massNumber of molelcules
Total (without water)25,9484
Polymers25,9484
Non-polymers00
Water0
1
D: synthetic DNA strand

D: synthetic DNA strand

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha

A: DNA-binding protein HU-alpha
B: DNA-binding protein HU-alpha

C: synthetic DNA strand

C: synthetic DNA strand


Theoretical massNumber of molelcules
Total (without water)71,02310
Polymers71,02310
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
crystal symmetry operation7_555y,x,-z+1/32
crystal symmetry operation12_545x,x-y-1,-z+1/62
Unit cell
Length a, b, c (Å)75.010, 75.010, 221.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsThe asymmetric unit is the same as the biological assembly

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Components

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


Mass: 9564.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupA, b4000, JW3964 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF2, UniProt: P0ACF0*PLUS
#2: DNA chain synthetic DNA strand


Mass: 3196.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain synthetic DNA strand


Mass: 3623.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
Sequence detailsDNA sample sequence used in experiment is 5'-GTTCAATTGTTGTTAACTTG-3'. But the asymmetric unit ...DNA sample sequence used in experiment is 5'-GTTCAATTGTTGTTAACTTG-3'. But the asymmetric unit contains multiple, out-of-register duplex positions, so the DNA chain is modeled according to averaged density.

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis-Tris pH 5.8, 30% PEG MME 550, 0.05 M CaCl2

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2013 / Details: Q315R
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.485→110.99 Å / Num. all: 5242 / Num. obs: 5242 / % possible obs: 99.9 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.298 / Net I/σ(I): 13.4 / Num. measured all: 104372
Reflection shellResolution: 3.485→3.497 Å / Redundancy: 21.76 % / Rmerge(I) obs: 1.924 / Mean I/σ(I) obs: 2.257 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUL

1mul


Resolution: 3.49→64.96 Å / Cor.coef. Fo:Fc: 0.8917 / Cor.coef. Fo:Fc free: 0.8897 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.54
Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all ...Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all nucleotides, and the DNA chain was built accordingly.
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 266 5.12 %RANDOM
Rwork0.22 ---
obs0.2223 5194 99.69 %-
Displacement parametersBiso max: 204.53 Å2 / Biso mean: 92.5232 Å2 / Biso min: 39.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.5445 Å20 Å20 Å2
2--2.5445 Å20 Å2
3----5.0891 Å2
Refine analyzeLuzzati coordinate error obs: 0.917 Å
Refinement stepCycle: LAST / Resolution: 3.49→64.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 455 0 0 1639
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d699SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes191HARMONIC5
X-RAY DIFFRACTIONt_it1692HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1809SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1692HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2363HARMONIC21.47
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion22.03
LS refinement shellResolution: 3.49→3.9 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2526 58 4.1 %
Rwork0.2158 1357 -
all0.2173 1415 -
obs--99.69 %
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)
15.3925-2.60020.61113.5944-0.98246.62990.3423-0.0727-0.2984-0.41080.2413-0.05050.78510.2503-0.5836-0.05950.1598-0.1721-0.1396-0.1594-0.142611.5219-16.040319.5672
22.7542-0.14330.21062.5102-0.624300.1271-0.1215-0.0898-0.3517-0.0986-0.0552-0.11090.4638-0.0285-0.0220.1327-0.11520.0769-0.0775-0.203216.2055-13.390223.1059
33.385-1.124-0.53020.66684.431314.9937-0.20450.57080.52890.0223-0.6188-0.2137-0.066-0.31580.82330.30290.0140.0754-0.1878-0.3074-0.231631.9748-24.924413.477
46.20281.5421-1.65123.33854.590800.2637-0.73480.3271-0.19610.43130.10610.6203-0.2655-0.6950.04570.083-0.11050.11550.0746-0.2624-6.1472-9.109737.0031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 90
2X-RAY DIFFRACTION2{ B|* }B1 - 90
3X-RAY DIFFRACTION3{ C|* }C1 - 11
4X-RAY DIFFRACTION4{ D|* }D1 - 12

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