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- PDB-2a11: Crystal Structure of Nuclease Domain of Ribonuclase III from Myco... -

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Basic information

Entry
Database: PDB / ID: 2a11
TitleCrystal Structure of Nuclease Domain of Ribonuclase III from Mycobacterium Tuberculosis
ComponentsRibonuclease III
KeywordsTRANSCRIPTION / TRANSLATION / HYDROLASE / ribonuclease / RNase III / nuclease domain / Structural Genomics / PSI / Protein Structure Initiative / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
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 / 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 motif / 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 motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribonuclease 3 / Ribonuclease 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsAkey, D.L. / Berger, J.M. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: Protein Sci. / Year: 2005
Title: Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A
Authors: Akey, D.L. / Berger, J.M.
History
DepositionJun 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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_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: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6373
Polymers25,5571
Non-polymers802
Water2,900161
1
A: Ribonuclease III
hetero molecules

A: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2746
Polymers51,1142
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area2650 Å2
ΔGint-44 kcal/mol
Surface area13760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.589, 72.589, 96.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1003-

HOH

DetailsThe second part of the biological assembly is generated by the two fold symmetry operator: -x, -y, -z+1/2

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Components

#1: Protein Ribonuclease III / E.C.3.1.26.3 / RNase III


Mass: 25556.984 Da / Num. of mol.: 1 / Fragment: Nuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: rnc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLyS
References: UniProt: P66666, UniProt: P9WH03*PLUS, ribonuclease III
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3000, 100 mM Ca-acetate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9793, 1.000, 1.100
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 20, 2002
ADSC QUANTUM 42CCDAug 4, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1ALS 8.3.1MADMx-ray1
2ALS 8.3.1SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
211
31.11
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
1166730.0481.0142.53097.3
2164770.0471.0282.53096.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.383090.510.0370.917
4.275.3897.410.0410.913
3.734.2798.710.0410.953
3.393.7399.210.0440.972
3.153.3999.610.0521.047
2.963.1599.910.0641.031
2.822.9699.810.0781.081
2.692.8299.910.11.063
2.592.6999.610.1181.095
2.52.5988.710.1381.075
5.383090.720.0381.033
4.275.3897.520.0410.994
3.734.2798.720.0411.011
3.393.7399.220.0431.014
3.153.3999.620.0520.944
2.963.1599.920.0641.033
2.822.9699.820.0761.071
2.692.8299.920.0981.075
2.592.6995.320.1111.052
2.52.5980.120.1331.089
ReflectionResolution: 2.1→50 Å / Num. all: 15593 / Num. obs: 15508 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.049 / Χ2: 0.973 / Net I/σ(I): 28
Reflection shellResolution: 2.1→2.18 Å / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 5 / Num. measured obs: 1517 / Χ2: 0.9 / % possible all: 99.6

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.979310.84-9.81
12 wavelength211.23-3.48
Phasing MAD set siteAtom type symbol: LAM1 / B iso: 60 / Fract x: 0.763 / Fract y: 0.754 / Fract z: 0.028 / Occupancy: 0.9

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Processing

Software
NameClassification
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2857 774 5 %RANDOM
Rwork0.2585 ---
all0.286 15593 --
obs0.286 15447 99.1 %-
Solvent computationBsol: 84.097 Å2
Displacement parametersBiso mean: 56.844 Å2
Baniso -1Baniso -2Baniso -3
1--3.355 Å20 Å20 Å2
2---3.355 Å20 Å2
3---6.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 2 161 1321
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_mcbond_it3.723
X-RAY DIFFRACTIONc_mcangle_it5.2154.5
X-RAY DIFFRACTIONc_scbond_it5.7294.5
X-RAY DIFFRACTIONc_scangle_it7.7266.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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