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- PDB-1o0w: Crystal structure of Ribonuclease III (TM1102) from Thermotoga ma... -

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Basic information

Entry
Database: PDB / ID: 1o0w
TitleCrystal structure of Ribonuclease III (TM1102) from Thermotoga maritima at 2.0 A resolution
ComponentsRibonuclease III
KeywordsHYDROLASE / TM1102 / Ribonuclease III / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


ribonuclease III / rRNA catabolic process / ribonuclease III activity / tRNA processing / RNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / rRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif ...Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ribonuclease III (TM1102) from Thermotoga maritima at 2.0 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300 BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ... BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease III
B: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)58,0662
Polymers58,0662
Non-polymers00
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-23 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36, 58.5, 70.2
Angle α, β, γ (deg.)67.2, 92, 77.7
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ribonuclease III / RNase III


Mass: 29033.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0I6, ribonuclease III
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.23 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / pH: 6.9
Details: 0.2 M Potassium Nitrate, 20% PEG 3350, pH 6.9, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.90

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979321, 0.978964, 0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793211
20.9789641
30.918371
ReflectionResolution: 1.995→34.899 Å / Num. obs: 32670 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.5 Å2 / Rsym value: 0.068 / Net I/σ(I): 11.6
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.27 / % possible all: 88.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
SnBphasing
MLPHAREphasing
CCP4model building
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→25 Å / Isotropic thermal model: ANISTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1631 4.7 %RANDOM
Rwork0.195 ---
obs0.195 32670 94.6 %-
all-32670 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 0.36 Å2 / ksol: 47.61 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.522 Å20.539 Å25.397 Å2
2--1.771 Å21.869 Å2
3---0.751 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 0 383 4234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4831.5
X-RAY DIFFRACTIONc_mcangle_it2.1922
X-RAY DIFFRACTIONc_scbond_it2.6522
X-RAY DIFFRACTIONc_scangle_it3.9722.5
LS refinement shellResolution: 2→2.02 Å / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.2875 59 6.1 %
Rwork0.2577 913 -

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