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- PDB-2dkf: Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RN... -

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Basic information

Entry
Database: PDB / ID: 2dkf
TitleCrystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily
Componentsmetallo-beta-lactamase superfamily protein
KeywordsHYDROLASE / beta-CASP family / metallo-beta-lactamase / ribonuclease / RNase E / Thermus thermophilus / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / SAD / Resolution: 2.8 Å
AuthorsIshikawa, I. / Nakagawa, N. / Kuramitsu, S. / Yokoyama, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem.(Tokyo) / Year: 2006
Title: Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily
Authors: Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionApr 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: metallo-beta-lactamase superfamily protein
B: metallo-beta-lactamase superfamily protein
C: metallo-beta-lactamase superfamily protein
D: metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,30912
Polymers189,7854
Non-polymers5238
Water1,65792
1
A: metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5773
Polymers47,4461
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5773
Polymers47,4461
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5773
Polymers47,4461
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5773
Polymers47,4461
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: metallo-beta-lactamase superfamily protein
C: metallo-beta-lactamase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1546
Polymers94,8932
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-162 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.220, 147.100, 121.230
Angle α, β, γ (deg.)90.00, 109.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
metallo-beta-lactamase superfamily protein / TTHA0252 protein


Mass: 47446.340 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 55771634, UniProt: Q5SLP1*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.52 %
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: 0.97882 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2005
RadiationMonochromator: transparent diamond double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97882 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 58051 / Num. obs: 58051 / % possible obs: 99.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 9.95 / Num. unique all: 5799 / Rsym value: 0.281 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.99 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 5673 -random
Rwork0.2417 ---
all-55906 --
obs-55906 96 %-
Displacement parametersBiso mean: 68.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-3.16 Å23.77 Å2
2--0 Å27.54 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13304 0 8 92 13404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.12
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.403 898 -
Rwork0.361 --
obs-8763 90.6 %

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