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- PDB-1jfz: Crystal Structure of MN(II)-Complex of RNAse III Endonuclease Dom... -

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Basic information

Entry
Database: PDB / ID: 1jfz
TitleCrystal Structure of MN(II)-Complex of RNAse III Endonuclease Domain from Aquifex Aeolicus at 2.10 Angstrom Resolution
ComponentsRIBONUCLEASE III
KeywordsHYDROLASE / RIBONUCLEASE / RNASE III / DOUBLE-STRANDED RNA / RNA INTERFERENCE / ENDONUCLEASE DOMAIN / ENDONUCLEOLYTIC CLEAVAGE
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / tRNA processing / RNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / regulation of gene expression / metal ion binding / identical protein binding / cytosol
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 domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / 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 domain / 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
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBlaszczyk, J. / Ji, X.
CitationJournal: Structure / Year: 2001
Title: Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage.
Authors: Blaszczyk, J. / Tropea, J.E. / Bubunenko, M. / Routzahn, K.M. / Waugh, D.S. / Court, D.L. / Ji, X.
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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
Revision 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE III
B: RIBONUCLEASE III
C: RIBONUCLEASE III
D: RIBONUCLEASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8728
Polymers72,6524
Non-polymers2204
Water12,827712
1
A: RIBONUCLEASE III
B: RIBONUCLEASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4364
Polymers36,3262
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-21 kcal/mol
Surface area14500 Å2
MethodPISA
2
C: RIBONUCLEASE III
D: RIBONUCLEASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4364
Polymers36,3262
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-21 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.741, 140.549, 49.759
Angle α, β, γ (deg.)90.00, 117.42, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. The asymmetric unit is composed from two independent dimers: first dimer is composed from identical chains A and B, and second dimer from identical chains C and D

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Components

#1: Protein
RIBONUCLEASE III / RNASE III


Mass: 18163.012 Da / Num. of mol.: 4 / Fragment: N-TERMINAL ENDONUCLEASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PKM803 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67082, ribonuclease III
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.13 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, TRIS-HCL, ACETATE, CHLORIDE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 18-20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mg/mlprotein1drop
20.6 M1dropNaCl
325 mMTris-HCl1droppH7.5
430 %(w/v)PEG40001reservoir
50.2 Msodium acetate1reservoir
60.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.045
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2001 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 33591 / Num. obs: 33591 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.165 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.3132
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.023 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 2.985 / Num. unique all: 2721 / % possible all: 74.7
Reflection
*PLUS
Num. measured all: 72740
Reflection shell
*PLUS
% possible obs: 74.7 % / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1I4S

1i4s


Resolution: 2.1→30 Å / Num. parameters: 21898 / Num. restraintsaints: 20454 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: LEAST-SQUARES REFINEMENT USING THE KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 1719 5.464 %RANDOM
Rwork0.1947 ---
all0.2079 31462 --
obs0.1891 26653 89.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975) 201-228
Displacement parametersBiso mean: 31.865 Å2
Refine analyzeLuzzati coordinate error obs: 0.228 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5640
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4948 0 4 712 5664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.034
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.085
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
2.1-2.210.255X-RAY DIFFRACTION3256
2.21-2.330.231X-RAY DIFFRACTION3100
2.33-2.460.219X-RAY DIFFRACTION3290
2.46-2.620.198X-RAY DIFFRACTION3128
2.62-2.810.185X-RAY DIFFRACTION3001
2.81-3.070.173X-RAY DIFFRACTION3096
3.07-3.470.168X-RAY DIFFRACTION3212
3.47-4.20.166X-RAY DIFFRACTION3124
4.2-6.850.179X-RAY DIFFRACTION3122
6.85-300.293X-RAY DIFFRACTION918
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / Rfactor all: 0.209 / Rfactor obs: 0.191 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.02
X-RAY DIFFRACTIONs_chiral_restr0.036

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