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- PDB-3ie0: Crystal Structure of S378Y mutant TTHA0252 from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 3ie0
TitleCrystal Structure of S378Y mutant TTHA0252 from Thermus thermophilus HB8
ComponentsRibonuclease TTHA0252
KeywordsHYDROLASE / Metallo beta lactamase fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Endonuclease / Metal-binding / Nuclease / RNA-binding / rRNA processing
Function / homology
Function and homology information


rRNA processing / endonuclease activity / 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 / Metallo-beta-lactamase / 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 / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Ribonuclease TTHA0252
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsIshikawa, H. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of S378Y mutant TTHA0252 from Thermus thermophilus HB8
Authors: Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 4, 2009ID: 2ZDD
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 1.4Nov 1, 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: Ribonuclease TTHA0252
B: Ribonuclease TTHA0252
C: Ribonuclease TTHA0252
D: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,30382
Polymers188,7774
Non-polymers7,52778
Water1,44180
1
A: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,62425
Polymers47,1941
Non-polymers2,43024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,33923
Polymers47,1941
Non-polymers2,14522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,15022
Polymers47,1941
Non-polymers1,95621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,19012
Polymers47,1941
Non-polymers99511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.181, 146.116, 121.004
Angle α, β, γ (deg.)90.000, 109.510, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ribonuclease TTHA0252


Mass: 47194.168 Da / Num. of mol.: 4 / Mutation: S378Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0252 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5SLP1, Hydrolases; Acting on ester bonds
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 67 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.16 Å3/Da / Density % sol: 61.08 % / Mosaicity: 0.266 °
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: 1.282245 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2007
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282245 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 61873 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.044 / Χ2: 1.065 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.73-2.833.90.30861840.927199.1
2.83-2.943.90.21361040.937199.2
2.94-3.073.90.14461610.964199.3
3.07-3.243.90.09761550.964199.4
3.24-3.443.90.06861731.013199.5
3.44-3.73.80.04961600.997199.7
3.7-4.083.80.03762481.022199.7
4.08-4.673.80.02961951.065199.8
4.67-5.883.80.0362351.1451100
5.88-503.70.0362581.642198.9

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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: 2.73→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
Rfree0.272 6035 9.7 %random
Rwork0.218 ---
obs-59828 96.1 %-
Solvent computationBsol: 38.53 Å2
Displacement parametersBiso max: 178.75 Å2 / Biso mean: 64.278 Å2 / Biso min: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.311 Å20 Å2-6.951 Å2
2--2.819 Å20 Å2
3----0.508 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13328 0 382 80 13790
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3761.5
X-RAY DIFFRACTIONc_scbond_it1.7872
X-RAY DIFFRACTIONc_mcangle_it2.3852
X-RAY DIFFRACTIONc_scangle_it2.8292.5
LS refinement shellResolution: 2.73→2.9 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.407 946 -
Rwork0.353 --
obs-9173 88.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep_glycis.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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