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- PDB-1vea: Crystal Structure of HutP, an RNA binding antitermination protein -

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Basic information

Entry
Database: PDB / ID: 1vea
TitleCrystal Structure of HutP, an RNA binding antitermination protein
ComponentsHut operon positive regulatory protein
KeywordsRNA BINDING PROTEIN / HutP / Antiterminator / regulation of transcription
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
N-(2-NAPHTHYL)HISTIDINAMIDE / Hut operon positive regulatory protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKumarevel, T.S. / Fujimoto, Z. / Karthe, P. / Oda, M. / Mizuno, H. / Kumar, P.K.R.
Citation
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.
#1: Journal: J.Struct.Biol. / Year: 2002
Title: Crystallization and preliminary X-ray diffraction studies of HutP protein: an RNA-binding protein that regulates the transcription of hut operon in Bacillus subtilis
Authors: Kumarevel, T.S. / Fujimoto, Z. / Padmanabhan, B. / Oda, M. / Nishikawa, S. / Mizuno, H. / Kumar, P.K.R.
#2: Journal: Mol.Microbiol. / Year: 2000
Title: cis-acting regulatory sequences for antitermination in the transcript of the Bacillus subtilis hut operon and histidine-dependent binding of HutP to the transcript containing the regulatory sequences
Authors: Oda, M. / Kobayashi, N. / Ito, A. / Kurusu, Y. / Taira, K.
History
DepositionMar 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7453
Polymers32,4652
Non-polymers2801
Water1,49583
1
A: Hut operon positive regulatory protein
B: Hut operon positive regulatory protein
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)98,2369
Polymers97,3956
Non-polymers8413
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 area15610 Å2
ΔGint-59 kcal/mol
Surface area32620 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: z,x,y and y,z,x.

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Components

#1: Protein Hut operon positive regulatory protein / HutP


Mass: 16232.553 Da / Num. of mol.: 2 / Fragment: RNA-binding, antiterminator protein / Mutation: V51I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET5a, pETHP4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10943
#2: Chemical ChemComp-HBN / N-(2-NAPHTHYL)HISTIDINAMIDE / L-HISTIDINE BETA NAPHTHYLAMIDE


Type: L-peptide linking / Mass: 280.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG2000MME, Pottasium bromide, Na Cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978, 1.007, 0.995, 0.950
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 3, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
21.0071
30.9951
40.951
ReflectionResolution: 2.8→31.803 Å / Num. all: 7375 / Num. obs: 7375 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 85.5 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.05 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7379 / Rsym value: 0.239 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→19.48 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1236996.06 / 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
Rfree0.281 398 5.4 %RANDOM
Rwork0.23 ---
obs0.23 7340 99.9 %-
all-7348 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.0642 Å2 / ksol: 0.259333 e/Å3
Displacement parametersBiso mean: 68.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 21 83 2247
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_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.861.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.426 53 4.4 %
Rwork0.341 1155 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BETA_NAPHTHYLAMIDE.PARAMBETA_NAPHTHYLAMIDE.TOP

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