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- PDB-3ie1: Crystal structure of H380A mutant TTHA0252 from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 3ie1
TitleCrystal structure of H380A mutant TTHA0252 from Thermus thermophilus HB8 complexed with RNA
Components
  • RNA (5'-R(P*UP*UP*UP*U)-3')
  • Ribonuclease TTHA0252
KeywordsHYDROLASE/RNA / 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 / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A ...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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / 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: 2.85 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 H380A mutant TTHA0252 from Thermus thermophilus HB8 complexed with RNA
Authors: Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 4, 2009ID: 2ZDE
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

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease TTHA0252
B: Ribonuclease TTHA0252
C: Ribonuclease TTHA0252
D: Ribonuclease TTHA0252
E: RNA (5'-R(P*UP*UP*UP*U)-3')
F: RNA (5'-R(P*UP*UP*UP*U)-3')
G: RNA (5'-R(P*UP*UP*UP*U)-3')
H: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,01272
Polymers192,9238
Non-polymers6,08964
Water68538
1
A: Ribonuclease TTHA0252
E: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,46924
Polymers48,2312
Non-polymers2,23822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-22 kcal/mol
Surface area17260 Å2
MethodPISA
2
B: Ribonuclease TTHA0252
F: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,99521
Polymers48,2312
Non-polymers1,76419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-24 kcal/mol
Surface area16690 Å2
MethodPISA
3
C: Ribonuclease TTHA0252
G: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,32214
Polymers48,2312
Non-polymers1,09112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-15 kcal/mol
Surface area17140 Å2
MethodPISA
4
D: Ribonuclease TTHA0252
H: RNA (5'-R(P*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,22613
Polymers48,2312
Non-polymers99511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-25 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.424, 148.165, 120.837
Angle α, β, γ (deg.)90.000, 109.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 2 types, 8 molecules ABCDEFGH

#1: Protein
Ribonuclease TTHA0252


Mass: 47051.008 Da / Num. of mol.: 4 / Mutation: H380A
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: RNA chain
RNA (5'-R(P*UP*UP*UP*U)-3')


Mass: 1179.706 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Non-polymers , 4 types, 102 molecules

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


Mass: 96.063 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#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.: 38 / 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: 3.13 Å3/Da / Density % sol: 60.76 % / Mosaicity: 0.448 °
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: BL26B2 / Wavelength: 1.28244 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2007
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28244 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 55129 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Χ2: 1.082 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.955.50.34154960.7511100
2.95-3.075.50.22554690.7521100
3.07-3.215.50.15254880.7651100
3.21-3.385.50.09955110.7941100
3.38-3.595.50.06855090.7981100
3.59-3.875.50.05255140.8761100
3.87-4.265.40.0555231.3371100
4.26-4.875.30.04754951.964199.8
4.87-6.145.30.03855511.41100
6.14-504.90.02755731.484199.3

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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: 2.85→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
Rfree0.291 5446 9.8 %random
Rwork0.231 ---
obs-53939 97.2 %-
Solvent computationBsol: 47.281 Å2
Displacement parametersBiso max: 171.43 Å2 / Biso mean: 75.373 Å2 / Biso min: 15.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.065 Å20 Å2-4.872 Å2
2---3.678 Å20 Å2
3----2.388 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13284 284 304 38 13910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3631.5
X-RAY DIFFRACTIONc_scbond_it1.7522
X-RAY DIFFRACTIONc_mcangle_it2.3692
X-RAY DIFFRACTIONc_scangle_it2.7842.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.408 832 -
Rwork0.353 --
obs-8274 89.6 %
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
X-RAY DIFFRACTION5dna-rna_rep_new.param

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