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- PDB-4ok9: Crystal structure of the single-stranded RNA binding protein HutP... -

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Basic information

Entry
Database: PDB / ID: 4ok9
TitleCrystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans
ComponentsHut operon positive regulatory protein
KeywordsRNA BINDING PROTEIN / Antitermination / Single stranded RNA binding protein
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 speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsThiruselvam, V. / Ponnuswamy, M.N. / Kumarevel, T.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans
Authors: Thiruselvam, V. / Sivaraman, P. / Kumarevel, T. / Ponnuswamy, M.N.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,06410
Polymers32,6052
Non-polymers4588
Water3,261181
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)99,19130
Polymers97,8166
Non-polymers1,37424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area20130 Å2
ΔGint-162 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.811, 90.811, 76.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-202-

MG

21A-203-

MG

31B-202-

MG

41B-203-

MG

51A-317-

HOH

61A-350-

HOH

71B-324-

HOH

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Components

#1: Protein Hut operon positive regulatory protein


Mass: 16302.699 Da / Num. of mol.: 2 / Fragment: HutP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Strain: NG80-2 / Gene: GTNG_0361, hutP / Production host: Escherichia coli (E. coli) / References: UniProt: A4IK89
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 10%(W/V) PEG300, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 23, 2013 / Details: Si II crystal
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 27972 / Num. obs: 27972 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 56
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1388 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZH0

2zh0
PDB Unreleased entry


Resolution: 1.91→35.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.315 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.131 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23187 1404 5 %RANDOM
Rwork0.1762 ---
obs0.17897 26549 99.83 %-
all-27972 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.348 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.35 Å20 Å2
2---0.35 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.91→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 28 181 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192308
X-RAY DIFFRACTIONr_bond_other_d0.0020.022266
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.963120
X-RAY DIFFRACTIONr_angle_other_deg0.95535172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37422.778108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32815390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5251524
X-RAY DIFFRACTIONr_chiral_restr0.1340.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
LS refinement shellResolution: 1.909→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 91 -
Rwork0.26 1952 -
obs--99.42 %

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