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- PDB-1huu: DNA-BINDING PROTEIN HU FROM BACILLUS STEAROTHERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1huu
TitleDNA-BINDING PROTEIN HU FROM BACILLUS STEAROTHERMOPHILUS
ComponentsPROTEIN HU
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DNA SUPERCOILING / ALPHA/BETA CLASS / MINOR GROOVE BINDER
Function / homology
Function and homology information


chromosome condensation / structural constituent of chromatin / DNA binding
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-binding protein HU / DNA-binding protein HU
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE ISOMORPHOUS REPLACEMENT PLUS ANOMALOUS (URANYL), NCS AVERAGING ON THREE MOLECULES / Resolution: 2 Å
AuthorsWhite, S.W. / Tanaka, I. / Appelt, K. / Wilson, K.S.
CitationJournal: Proteins / Year: 1989
Title: A protein structural motif that bends DNA.
Authors: White, S.W. / Appelt, K. / Wilson, K.S. / Tanaka, I.
History
DepositionJul 6, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN HU
B: PROTEIN HU
C: PROTEIN HU


Theoretical massNumber of molelcules
Total (without water)29,2003
Polymers29,2003
Non-polymers00
Water4,882271
1
A: PROTEIN HU

A: PROTEIN HU


Theoretical massNumber of molelcules
Total (without water)19,4662
Polymers19,4662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3560 Å2
ΔGint-41 kcal/mol
Surface area9250 Å2
MethodPISA, PQS
2
B: PROTEIN HU


Theoretical massNumber of molelcules
Total (without water)9,7331
Polymers9,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN HU


Theoretical massNumber of molelcules
Total (without water)9,7331
Polymers9,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: PROTEIN HU

B: PROTEIN HU


Theoretical massNumber of molelcules
Total (without water)19,4662
Polymers19,4662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
5
C: PROTEIN HU

C: PROTEIN HU


Theoretical massNumber of molelcules
Total (without water)19,4662
Polymers19,4662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)65.500, 37.300, 65.500
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.116, -0.0006, 0.9933), (0.0023, 1, 0.0003), (-0.9933, 0.0022, 0.116)19.1822, 12.4329, 29.76
2given(0.9402, -0.0016, -0.3406), (0.0008, 1, -0.0024), (0.3406, 0.0019, 0.9402)42.0819, 12.1478, 6.3987
3given(-0.2293, 0.0001, -0.9734), (0.001, 1, -0.0001), (0.9734, -0.001, -0.2293)25.8591, -0.3501, 20.0352
DetailsTHE ASYMMETRIC UNIT CONSISTS OF THREE HU MONOMERS ARRANGED AROUND THREE OF THE FOUR TWOFOLD AXES IN THE P2 SPACE GROUP. BIOLOGICALLY RELEVANT DIMERS ARE GENERATED BY THE SYMMETRY OPERATIONS OF THE UNIT CELL. THE SOLVENT MOLECULES ARE LABELED ACCORDING TO THE MONOMER WITH WHICH THEY ASSOCIATE. WATER MOLECULES 100 THROUGH 135 ARE COMMON TO ALL THREE MOLECULES IN THE ASYMMETRIC UNIT AND CAN BE CONSIDERED STRUCTURAL. WATER MOLECULES 200 AND HIGHER ARE NOT COMMON TO ALL THREE MOLECULES.

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Components

#1: Protein PROTEIN HU / BSB / NS


Mass: 9733.168 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P02346, UniProt: P0A3H0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROTEIN HU BINDS DNA NON-SPECIFICALLY AND INTRODUCES SHARP BENDS. THE PROTEIN APPEARS TO INDUCE DNA ...PROTEIN HU BINDS DNA NON-SPECIFICALLY AND INTRODUCES SHARP BENDS. THE PROTEIN APPEARS TO INDUCE DNA NEGATIVE SUPERCOILING BY PROTEIN-PROTEIN INTERACTION. BIOLOGICAL ROLE IS TO INDUCE DNA SUPERCOILING AND RELIEVE TORSIONAL STRESS RESULTING FROM DNA PROCESSES SUCH AS TRANSCRIPTION AND REPLICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 51 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: unknown / PH range low: 9 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein11
225 mMphosphate11
335 %MPD12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: FILM / Detector: FILM / Date: Jul 1, 1983 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 18328 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2→2.19 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.1 / % possible all: 80
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT PLUS ANOMALOUS (URANYL), NCS AVERAGING ON THREE MOLECULES
Resolution: 2→6 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE MOLECULE CONTAINS A DISORDERED ARM REGION THAT IS KNOWN TO BIND DNA IN THE MINOR GROOVE FROM THE RELATED IHF STRUCTURE. EACH OF THE THREE MOLECULES IN THE ASYMMETRIC UNIT IS MISSING ...Details: THE MOLECULE CONTAINS A DISORDERED ARM REGION THAT IS KNOWN TO BIND DNA IN THE MINOR GROOVE FROM THE RELATED IHF STRUCTURE. EACH OF THE THREE MOLECULES IN THE ASYMMETRIC UNIT IS MISSING DIFFERENT AMOUNTS OF THE ARM DUE TO THE LACK OF ELECTRON DENSITY. MOLECULE A IS MISSING 59 THROUGH 68, MOLECULE B 57 THROUGH 72, AND MOLECULE C 56 THROUGH 74.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 333 10 %RANDOM
Rwork0.193 ---
obs0.193 17251 89 %-
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 271 1971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.19 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.33 55 12 %
Rwork0.289 1743 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2

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