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- PDB-3ie2: Crystal Structure of H400V mutant TTHA0252 from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 3ie2
TitleCrystal Structure of H400V 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


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 superfamily ...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 superfamily / 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
Ribonuclease TTHA0252
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 H400V 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: 2YVD
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)195,03174
Polymers188,3164
Non-polymers6,71570
Water1,40578
1
A: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,65927
Polymers47,0791
Non-polymers2,58026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,97021
Polymers47,0791
Non-polymers1,89120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,48916
Polymers47,0791
Non-polymers1,41015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease TTHA0252
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,91310
Polymers47,0791
Non-polymers8349
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.439, 149.738, 122.118
Angle α, β, γ (deg.)90.000, 110.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ribonuclease TTHA0252


Mass: 47079.059 Da / Num. of mol.: 4 / Mutation: H400V
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


Mass: 96.063 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.26 Å3/Da / Density % sol: 62.26 % / Mosaicity: 0.473 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.0M Ammonium Sulfate, 1%(w/v) Polyethylene Glycol 3350, 0.1M Bis-Tris, 4%(v/v) 2,2,2 Trifluoroethanol, pH 5.5, 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: 1.2824 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2007
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 55276 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Χ2: 1.629 / Net I/σ(I): 23.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.93.60.29358351.181199.6
2.9-3.023.70.20858731.204199.8
3.02-3.153.70.14358471.272199.9
3.15-3.323.80.10159231.3571100
3.32-3.533.80.08158731.7231100
3.53-3.83.30.0733112.108156.2
3.8-4.183.60.04948032.209181.3
4.18-4.793.80.0359081.6291100
4.79-6.033.80.0359361.7691100
6.03-503.70.02859672.192199.5

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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: 2.8→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
Rfree0.275 5345 9 %random
Rwork0.219 ---
obs-52852 89 %-
Solvent computationBsol: 35.067 Å2
Displacement parametersBiso max: 172.21 Å2 / Biso mean: 60.007 Å2 / Biso min: 7.32 Å2
Baniso -1Baniso -2Baniso -3
1-5.745 Å20 Å2-0.19 Å2
2---2.637 Å20 Å2
3----3.107 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13292 0 343 78 13713
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3041.5
X-RAY DIFFRACTIONc_scbond_it1.7562
X-RAY DIFFRACTIONc_mcangle_it2.2552
X-RAY DIFFRACTIONc_scangle_it2.7792.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.399 857 -
Rwork0.318 --
obs-8642 87.6 %
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

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