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- PDB-4pt4: Crystal structure Analysis of N terminal region containing the di... -

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Basic information

Entry
Database: PDB / ID: 4pt4
TitleCrystal structure Analysis of N terminal region containing the dimerization domain and DNA binding domain of HU protein(Histone like protein-DNA binding) from Mycobacterium tuberculosis [H37Ra]
ComponentsDNA-binding protein HU homolog
KeywordsDNA BINDING PROTEIN / DIMERIZATION BY FOUR HELIX BUNDLE INTERACTION / DNA condensation / DNA-binding
Function / homology
Function and homology information


biofilm matrix assembly / : / cellular response to iron ion starvation / DNA protection / nucleoid / chromosome condensation / supercoiled DNA binding / DNA-binding transcription activator activity / ferroxidase / ferroxidase activity ...biofilm matrix assembly / : / cellular response to iron ion starvation / DNA protection / nucleoid / chromosome condensation / supercoiled DNA binding / DNA-binding transcription activator activity / ferroxidase / ferroxidase activity / ferric iron binding / peptidoglycan-based cell wall / iron ion transport / protein-DNA complex / cell wall organization / structural constituent of chromatin / double-stranded DNA binding / damaged DNA binding / intracellular iron ion homeostasis / oxidoreductase activity / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / DNA binding / extracellular region / plasma 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
FORMIC ACID / DNA-binding protein HupB / DNA-binding protein HupB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBhowmick, T. / Ramagopal, U.A. / Ghosh, S. / Nagaraja, V. / Ramakumar, S.
CitationJournal: Nat Commun / Year: 2014
Title: Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors
Authors: Bhowmick, T. / Ghosh, S. / Dixit, K. / Ganesan, V. / Ramagopal, U.A. / Dey, D. / Sarma, S.P. / Ramakumar, S. / Nagaraja, V.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 21, 2014ID: 3C4I
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 26, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity_name_com ...database_2 / entity_name_com / entity_src_gen / pdbx_database_related / struct / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_related.details / _struct.title / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,5296
Polymers21,3442
Non-polymers1844
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-39 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.774, 53.974, 41.732
Angle α, β, γ (deg.)90.000, 97.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-binding protein HU homolog / Histone-like protein


Mass: 10672.215 Da / Num. of mol.: 2
Fragment: N terminal UNP residues 1-99 (dimerization domain and DNA binding domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Gene: hupB, MRA_3015 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A5U6Z7, UniProt: P9WMK7*PLUS
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.93 Å3/Da / Density % sol: 36.13 % / Mosaicity: 1.172 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 3M Sodium formate, 0.1M Tris-Cl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2007 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator (Cryogenically cooled)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 10304 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Χ2: 1.078 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.04-2.123.40.3919670.79792.9
2.12-2.213.60.34310100.90197.5
2.21-2.313.70.27410160.96199.1
2.31-2.433.90.24410400.92699.5
2.43-2.5840.20410290.98599.6
2.58-2.7840.1510361.02399.5
2.78-3.0640.10210301.12899.7
3.06-3.5140.07710441.2299.8
3.51-4.423.90.0610521.3199.8
4.42-503.70.06110801.43399.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P71

1p71


Resolution: 2.04→41.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2366 / WRfactor Rwork: 0.1766 / FOM work R set: 0.7719 / SU B: 15.753 / SU ML: 0.183 / SU R Cruickshank DPI: 0.2594 / SU Rfree: 0.2072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 491 4.8 %RANDOM
Rwork0.1877 ---
obs0.1906 10291 98.32 %-
all-10468 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.19 Å2 / Biso mean: 34.753 Å2 / Biso min: 18.77 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å2-0 Å21.14 Å2
2---1.82 Å20 Å2
3---3.44 Å2
Refine analyzeLuzzati coordinate error obs: 0.249 Å
Refinement stepCycle: LAST / Resolution: 2.04→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 12 86 1563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191491
X-RAY DIFFRACTIONr_bond_other_d0.0010.021507
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9582009
X-RAY DIFFRACTIONr_angle_other_deg0.77133432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3821.80361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03415252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8131520
X-RAY DIFFRACTIONr_chiral_restr0.0820.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_mcbond_it2.0793.047782
X-RAY DIFFRACTIONr_mcbond_other2.0773.048783
X-RAY DIFFRACTIONr_mcangle_it3.1544.555974
LS refinement shellResolution: 2.037→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 33 -
Rwork0.271 618 -
all-651 -
obs--85.66 %
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)
10.4088-0.02930.17150.0342-0.06390.1783-0.00340.0301-0.02070.0020.0107-0.0023-0.01140.0077-0.00730.0262-0.00440.00160.0176-0.00630.002516.51519.0224-2.3187
20.5462-0.0436-0.01580.02840.02380.0757-0.0262-0.03340.02450.01030.0143-0.00090.01880.02270.01190.0197-0.00260.00310.01930.00040.003816.2236.11122.5959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 244
2X-RAY DIFFRACTION2B1 - 242

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