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- PDB-1wro: Metal Ion dependency of the antiterminator protein, HutP, for bin... -

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Basic information

Entry
Database: PDB / ID: 1wro
TitleMetal Ion dependency of the antiterminator protein, HutP, for binding to the terminator region of hut mRNA- A structural basis
ComponentsHut operon positive regulatory protein
KeywordsRNA BINDING PROTEIN / HutP / Antitermination / L-histidine / metal ions / conformational change
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 / Hut operon positive regulatory protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKumarevel, T. / Mizuno, H. / Kumar, P.K.R.
Citation
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.
#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: Derived calculations / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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.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
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)49,59712
Polymers48,3043
Non-polymers1,2929
Water4,324240
1
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
C: Hut operon positive regulatory protein
hetero molecules

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)99,19324
Polymers96,6086
Non-polymers2,58518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area22040 Å2
ΔGint-226 kcal/mol
Surface area28380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.220, 81.140, 75.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe biological assembly is a hexamer generated from thr trimer in the asymmetric unit by the operation 1-x, -y, z (2_655)

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Components

#1: 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) / Plasmid: pET5a / Production host: Escherichia coli (E. coli) / Strain (production host): pETHP4 / References: UniProt: P10943
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-HIS / HISTIDINE


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


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: BaCl2, MPD, HEPES , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: May 19, 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: 2.35→50 Å / Num. all: 20744 / Num. obs: 20744 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.384 / Num. unique all: 2026 / % 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: 2.35→19.6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1433303.8 / 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
Rfree0.3 1048 5.1 %RANDOM
Rwork0.247 ---
obs0.247 20669 99.7 %-
all-20744 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7282 Å2 / ksol: 0.289893 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å20 Å2
2--1.81 Å20 Å2
3----4.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 39 240 3609
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 156 4.6 %
Rwork0.312 3207 -
obs--99.7 %
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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