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

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Basic information

Entry
Database: PDB / ID: 1wpt
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


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: 2.7 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: 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. / 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: 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
Water1,20767
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_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area13030 Å2
ΔGint-62 kcal/mol
Surface area34470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.410, 95.410, 95.410
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 / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.3 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG2K, MME, HEPES, MgCl2, 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: Oct 22, 2003
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: 2.6→50 Å / Num. all: 8514 / Num. obs: 8514 / % possible obs: 93.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.2 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.041
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.35 / Num. unique all: 874 / % 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: 2.7→19.48 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1778712.12 / 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
Rfree0.286 542 7.2 %RANDOM
Rwork0.228 ---
obs0.228 7492 92 %-
all-8514 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5798 Å2 / ksol: 0.307322 e/Å3
Displacement parametersBiso mean: 63 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 0 67 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it2.021.5
X-RAY DIFFRACTIONc_mcangle_it3.672
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.372.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.425 104 8 %
Rwork0.33 1202 -
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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