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- PDB-3boy: Crystal structure of the HutP antitermination complex bound to th... -

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Basic information

Entry
Database: PDB / ID: 3boy
TitleCrystal structure of the HutP antitermination complex bound to the HUT mRNA
Components
  • 5'-R(*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*U)-3'
  • Hut operon positive regulatory protein
KeywordsTRANSCRIPTION/RNA / HutP / RNA-binding / HutP-RNA Complex / Anti-termination / Transcription regulation / Activator / Histidine metabolism / TRANSCRIPTION-RNA COMPLEX / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / RNA (> 10) / Hut operon positive regulatory protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKumarevel, T.S. / Balasundaresan, D. / Jeyakanthan, J. / Shinkai, A. / Yokoyama, S. / Kumar, P.K.R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: To be Published
Title: Crystal Structure of HutP complexed with the 55-mer RNA
Authors: Kumarevel, T. / Balasundaresan, D. / Jeyakanthan, J. / Shinkai, A. / Yokoyama, S. / 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. / 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. / Gopinath, S.C.B. / Nishikawa, S. / Mizuno, H. / Kumar, P.K.R.
#3: 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.
#4: Journal: Nucleic Acids Res. / Year: 2005
Title: Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis
Authors: Kumarevel, T. / Mizuno, H. / Kumar, P.K.R.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 15, 2008ID: 2GZT
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 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
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.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.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.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_ref_seq_dif.details
Revision 1.4Nov 1, 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
D: 5'-R(*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*U)-3'
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
C: Hut operon positive regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,72210
Polymers55,1814
Non-polymers5416
Water7,314406
1
D: 5'-R(*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*U)-3'
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
C: Hut operon positive regulatory protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)111,44520
Polymers110,3628
Non-polymers1,08312
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.635, 76.469, 62.790
Angle α, β, γ (deg.)90.00, 109.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 6876.931 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Hut operon positive regulatory protein / HutP


Mass: 16101.357 Da / Num. of mol.: 3 / Mutation: V51I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: hutP / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 40% MPD, 0.1M HEPES, 0.1M MGCL2, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2HEPES11
3MgCl211
4H2O11
5MPD12
6HEPES12
7MgCl212
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2006
RadiationMonochromator: SI II Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 48341 / Num. obs: 48341 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.362 / Num. unique all: 4735 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WMQ

1wmq


Resolution: 1.7→38.24 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.627 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24629 2445 5.1 %RANDOM
Rwork0.19757 ---
all0.20004 45893 --
obs0.20004 45893 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.961 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 435 36 406 4270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213905
X-RAY DIFFRACTIONr_angle_refined_deg1.562.1035352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53322.95139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58815589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9021525
X-RAY DIFFRACTIONr_chiral_restr0.1030.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022743
X-RAY DIFFRACTIONr_nbd_refined0.2110.21868
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2306
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.2144
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.262
X-RAY DIFFRACTIONr_mcbond_it1.071.52231
X-RAY DIFFRACTIONr_mcangle_it1.65223434
X-RAY DIFFRACTIONr_scbond_it2.29131977
X-RAY DIFFRACTIONr_scangle_it3.6274.51918
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 169 -
Rwork0.268 3241 -
obs--95.44 %

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