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- PDB-1wps: Crystal Structure of HutP, an RNA binding anti-termination protein -

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Basic information

Entry
Database: PDB / ID: 1wps
TitleCrystal Structure of HutP, an RNA binding anti-termination protein
ComponentsHut operon positive regulatory protein
KeywordsRNA BINDING PROTEIN / HutP / RNA binding / Antitermination / Transcription regulation
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
Hut operon positive regulatory protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKumarevel, T.S. / Mizuno, H. / Kumar, P.K.R.
Citation
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.
#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 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein


Theoretical massNumber of molelcules
Total (without water)32,2032
Polymers32,2032
Non-polymers00
Water1,65792
1
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein

A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein

A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein


Theoretical massNumber of molelcules
Total (without water)96,6086
Polymers96,6086
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area14400 Å2
ΔGint-72 kcal/mol
Surface area35440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.820, 96.820, 96.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations:-1/2+z, -1/2-x, -y and -1/2-y, -z, 1/2+x

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Components

#1: 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.4 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG550, Bicine, EDTA, pH 7.6, 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: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→39.53 Å / Num. all: 7867 / Num. obs: 7867 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: -0.1 Å2 / Rmerge(I) obs: 0.137
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 6 % / Rmerge(I) obs: 0.3 / Num. unique all: 622 / % possible all: 89.4

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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: 2.8→19.76 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 89887.53 / 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
Rfree0.26 480 6.3 %RANDOM
Rwork0.207 ---
obs0.207 7656 99.8 %-
all-7867 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.3929 Å2 / ksol: 0.239494 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 0 92 2287
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it3.461.5
X-RAY DIFFRACTIONc_mcangle_it5.662
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 76 6 %
Rwork0.274 1186 -
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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