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- PDB-3iem: Crystal Structure of TTHA0252 from Thermus thermophilus HB8 compl... -

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Basic information

Entry
Database: PDB / ID: 3iem
TitleCrystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog
Components
  • RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
  • Ribonuclease TTHA0252
KeywordsHYDROLASE/RNA / metallo beta lactamase fold / Endonuclease / Hydrolase / Metal-binding / Nuclease / RNA-binding / rRNA processing / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #10890 / : / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Rossmann fold - #10890 / : / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / RNA / Ribonuclease TTHA0252
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIshikawa, H. / Nakagawa, N. / Kuramitus, S. / Yokoyama, S. / Masui, R.
CitationJournal: To be Published
Title: Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog
Authors: Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Ribonuclease TTHA0252
B: Ribonuclease TTHA0252
C: Ribonuclease TTHA0252
D: Ribonuclease TTHA0252
G: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
H: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
I: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
J: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
K: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
L: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
M: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
N: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
O: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
P: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,73782
Polymers207,35714
Non-polymers6,38068
Water4,035224
1
A: Ribonuclease TTHA0252
G: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
J: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
L: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
N: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,43624
Polymers54,6725
Non-polymers1,76419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease TTHA0252
H: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
K: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,04025
Polymers50,8953
Non-polymers2,14522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease TTHA0252
O: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
P: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,17917
Polymers50,8953
Non-polymers1,28414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease TTHA0252
I: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
M: RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08216
Polymers50,8953
Non-polymers1,18813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.694, 146.441, 119.975
Angle α, β, γ (deg.)90.00, 110.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-447-

SO4

21M-233-

HOH

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Components

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Protein / RNA chain , 2 types, 14 molecules ABCDGHIJKLMNOP

#1: Protein
Ribonuclease TTHA0252


Mass: 47118.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0252 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5SLP1, Hydrolases; Acting on ester bonds
#2: RNA chain
RNA (5'-R(*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU)P*(SSU))-3')


Mass: 1888.433 Da / Num. of mol.: 10 / Source method: obtained synthetically / Details: chemically-synthesized

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Non-polymers , 4 types, 292 molecules

#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 59 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSSU 1 IN CHAIN G, H, I, J, L, N SEEMS TO BE CLEAVED BY THE PROTEIN. SO O3'(SSU 1) IS PRESUMED OP3(SSU 2).

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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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50mM sodium citrate, 0.2M ammonium sulfate, 0.6M lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 18, 2008
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 80389 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.345 / Num. unique all: 8009 / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
XFITdata reduction
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DKF
Resolution: 2.5→50 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 7617 -random
Rwork0.213 ---
obs-75836 93.8 %-
Displacement parametersBiso mean: 51.083 Å2
Baniso -1Baniso -2Baniso -3
1-1.202 Å20 Å2-1.811 Å2
2---0.819 Å20 Å2
3----0.384 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13304 510 316 224 14354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.34
X-RAY DIFFRACTIONc_scbond_it1.94
X-RAY DIFFRACTIONc_mcangle_it2.257
X-RAY DIFFRACTIONc_scangle_it2.94
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.335 1134 -
Rwork0.29 --
obs-11144 83.1 %

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