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- PDB-1wrq: Crystal Structure of HutP-Antitermination complex -

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Basic information

Entry
Database: PDB / ID: 1wrq
TitleCrystal Structure of HutP-Antitermination complex
Components
  • 5'-R(*UP*UP*UP*AP*GP*UP*U)-3'
  • Hut operon positive regulatory protein
KeywordsTRANSCRIPTION/RNA / HutP / RNA binding protein / Antitermination / L-histidine / metal ions / conformational change / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


L-histidine metabolic process / 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: 2.2 Å
AuthorsKumarevel, T. / Mizuno, H. / Kumar, P.K.R.
Citation
Journal: To be published
Title: Crystal Structure of the HutP-antitermination complex
Authors: Kumarevel, T. / Mizuno, H. / Kumar, P.K.R.
#1: Journal: Nature / Year: 2005
Title: Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand
Authors: Kumarevel, T. / Mizuno, H. / Kumar, P.K.R.
#2: 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. / Fujimoto, Z. / Karthe, P. / Oda, M. / Mizuno, H. / Kumar, P.K.R.
#3: 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. / Gopinath, S.C.B. / Nishikawa, S. / Mizuno, H. / Kumar, P.K.R.
History
DepositionOct 25, 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 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
C: 5'-R(*UP*UP*UP*AP*GP*UP*U)-3'
D: 5'-R(*UP*UP*UP*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)36,8848
Polymers36,5234
Non-polymers3614
Water5,657314
1
C: 5'-R(*UP*UP*UP*AP*GP*UP*U)-3'
D: 5'-R(*UP*UP*UP*AP*GP*UP*U)-3'
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
hetero molecules

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

C: 5'-R(*UP*UP*UP*AP*GP*UP*U)-3'
D: 5'-R(*UP*UP*UP*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)110,65324
Polymers109,57012
Non-polymers1,08312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)75.800, 75.800, 133.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-3042-

HOH

Detailsthe biological assembly is a hexamer generated from thr trimer in the asymmetric unit by the following operations, -y, x-y, z (2_555) and -x+y, -x, z (3_555)

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Components

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


Mass: 2160.283 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 / Production host: Escherichia coli (E. coli) / Strain (production host): pETHP4 / 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.: 314 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Nacacodylate, KBr, PEG 2KMME, MgCl2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Nacacodylate11
2KBr11
3PEG11
4MgCl211
5MgCl212

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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 12, 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: 2.2→40 Å / Num. all: 14514 / Num. obs: 14514 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.233 / Num. unique all: 2124 / % possible all: 100

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Processing

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

1vea


Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1853239.72 / 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
Rfree0.243 724 5 %RANDOM
Rwork0.198 ---
obs0.198 14503 99.9 %-
all-14514 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.2854 Å2 / ksol: 0.363519 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.17 Å2-1.28 Å20 Å2
2---5.17 Å20 Å2
3---10.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 284 24 314 2823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d2.52
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 105 4.3 %
Rwork0.222 2320 -
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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