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

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Basic information

Entry
Database: PDB / ID: 3iel
TitleCrystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP
ComponentsRibonuclease TTHA0252
KeywordsHYDROLASE / metallo beta lactamase fold / Endonuclease / Metal-binding / Nuclease / RNA-binding / rRNA processing
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 / URIDINE-5'-MONOPHOSPHATE / Ribonuclease TTHA0252
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsIshikawa, H. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R.
CitationJournal: To be Published
Title: Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP
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, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease TTHA0252
B: Ribonuclease TTHA0252
C: Ribonuclease TTHA0252
D: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,865117
Polymers188,4724
Non-polymers12,393113
Water5,152286
1
A: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,48539
Polymers47,1181
Non-polymers4,36638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,29629
Polymers47,1181
Non-polymers3,17828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,97529
Polymers47,1181
Non-polymers2,85728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,11020
Polymers47,1181
Non-polymers1,99219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.238, 146.677, 120.349
Angle α, β, γ (deg.)90.000, 110.110, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 399 molecules

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


Mass: 96.063 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.19 Å3/Da / Density % sol: 61.48 % / Mosaicity: 0.416 °
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: Jul 23, 2009
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: 2.35→50 Å / Num. obs: 97950 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.039 / Χ2: 1.154 / Net I/σ(I): 22.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.435.60.3497541.02199.9
2.43-2.535.60.26897591.03199.9
2.53-2.655.70.19498031.031100
2.65-2.795.70.14398131.034100
2.79-2.965.80.09897661.067100
2.96-3.195.80.06397791.11100
3.19-3.515.80.03998051.156100
3.51-4.025.80.0398271.29499.9
4.02-5.065.70.02498481.2999.9
5.06-505.50.02497961.51398.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DKF

2dkf


Resolution: 2.35→50 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 9357 9.5 %random
Rwork0.222 ---
obs-93725 95.3 %-
Solvent computationBsol: 49.926 Å2
Displacement parametersBiso max: 186.63 Å2 / Biso mean: 59.929 Å2 / Biso min: 16.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.595 Å20 Å2-2.242 Å2
2---5.084 Å20 Å2
3---4.488 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13304 0 661 286 14251
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4171.5
X-RAY DIFFRACTIONc_scbond_it1.9962
X-RAY DIFFRACTIONc_mcangle_it2.3192
X-RAY DIFFRACTIONc_scangle_it2.9732.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.352 1438 -
Rwork0.303 --
obs-14321 88.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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