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- PDB-1wpu: Crystal Structure of the HutP antitermination complex bound to a ... -

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Basic information

Entry
Database: PDB / ID: 1wpu
TitleCrystal Structure of the HutP antitermination complex bound to a single stranded region of hut mRNA
Components
  • 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
  • Hut operon positive regulatory protein
KeywordsTRANSCRIPTION/RNA / HutP / RNA binding / HutP-RNA complex / Antitermination / Transcription regulation / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


: / mRNA binding / positive regulation of gene expression
Similarity search - Function
Hut operon positive regulatory protein HutP / Hut operon regulatory protein HutP / Hut operon regulatory protein HutP / Hut operon regulatory protein HutP, bacillales / Hut operon regulatory protein HutP superfamily / HutP / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / RNA / Hut operon positive regulatory protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKumarevel, T.S. / Mizuno, H. / Kumar, P.K.R.
Citation
Journal: To be Published
Title: Structural basis for the HutP antitermination Complex:Role of divalent metal ions in allosteric activation
Authors: Kumarevel, T.S. / Mizuno, H. / Kumar, P.K.R.
#1: Journal: Structure / Year: 2004
Title: Crystal Structure of Activated HutP; An RNA Binding Protein that Regulates Transcription of the hut Operon in Bacillus subtilis
Authors: Kumarevel, T.S. / Fujimoto, Z. / Karthe, P. / Oda, M. / Mizuno, H. / Kumar, P.K.R.
#2: Journal: NUCLEIC ACIDS RES. / Year: 2004
Title: Identification of important chemical groups of the hut mRNA for HutP interactions that regulate the hut operon in Bacillus subtilis
Authors: Kumarevel, T.S. / Gopinath, S.C. / Nishikawa, S. / Mizuno, H. / Kumar, P.K.
History
DepositionSep 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 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
C: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
D: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9628
Polymers36,6014
Non-polymers3614
Water7,278404
1
C: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
D: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
hetero molecules

C: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
D: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
hetero molecules

C: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
D: 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,88724
Polymers109,80412
Non-polymers1,08312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Unit cell
Length a, b, c (Å)76.060, 76.060, 133.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z

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Components

#1: RNA chain 5'-R(*UP*UP*GP*AP*GP*UP*U)-3'


Mass: 2199.323 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Hut operon positive regulatory protein / HutP


Mass: 16101.357 Da / Num. of mol.: 2 / Mutation: V51I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET5a, pETHP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10943
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 1.7 Å3/Da / Density % sol: 26.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MPD, HEPES, MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2HEPES11
3MgCl211
4MPD12
5HEPES12
6MgCl212

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 47155 / Num. obs: 47155 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.314 / Num. unique all: 4826 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VEA

1vea


Resolution: 1.48→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1551356.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2338 5 %RANDOM
Rwork0.214 ---
obs0.214 46982 97.5 %-
all-47155 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.8352 Å2 / ksol: 0.359595 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20.01 Å20 Å2
2---0.58 Å20 Å2
3---1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.48→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 290 24 404 2936
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 1.48→1.57 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 416 5.2 %
Rwork0.257 7596 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMDNA-RNA_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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