PDB-2c0b: Catalytic domain of E. coli RNase E in complex with 13-mer RNA

Basic information

• Entry: Database: PDB / ID: 2c0b
• Title: Catalytic domain of E. coli RNase E in complex with 13-mer RNA

Components

• 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'
• RIBONUCLEASE E

• Keywords: HYDROLASE / RIBONUCLEASE / RNA TURNOVER / RNA PROCESSING / ENDONUCLEASE / NUCLEASE / RNA-BINDING

Function / homology

Function:

regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / rRNA binding / molecular adaptor activity / magnesium ion binding / RNA binding / zinc ion binding / membrane / identical protein binding / cytoplasm

Domain/homology:

Ribonuclease E, catalytic domain / Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / Hypothetical Protein Ychn; Chain: A, / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

RNA / RNA (> 10) / Ribonuclease E

• Biological species: ESCHERICHIA COLI (E. coli); SYNTHETIC CONSTRUCT (others)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
• Authors: Marcaida, M.J. / Callaghan, A.J. / Scott, W.G. / Luisi, B.F.
• Citation: Journal: Nature / Year: 2005; Title: Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover; Authors: Callaghan, A.J. / Marcaida, M.J. / Stead, J.A. / Mcdowall, K.J. / Scott, W.G. / Luisi, B.F.

History

Deposition	Aug 30, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 14, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2015	Group: Atomic model / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

L: RIBONUCLEASE E

R: 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'

hetero molecules

Summary:

• 62.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	62,411	5
Polymers	62,297	2
Non-polymers	114	3
Water	883	49

1

L: RIBONUCLEASE E

R: 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'

hetero molecules

L: RIBONUCLEASE E

R: 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'

hetero molecules

L: RIBONUCLEASE E

R: 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'

hetero molecules

L: RIBONUCLEASE E

R: 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'

hetero molecules

Summary:

• defined by author&software
• 250 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	249,642	20
Polymers	249,186	8
Non-polymers	456	12
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_545	-x,-y-1,z	1
crystal symmetry operation	12_545	x,x-y-1,-z+1/3	1
crystal symmetry operation	9_555	-x,-x+y,-z+1/3	1

Calculated values:

Method	PQS

Unit cell

Length a, b, c (Å)	196.049, 196.049, 142.660
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	180
Space group name H-M	P6222

Components on special symmetry positions

ID	Model	Components
1	1	L-1511- ZN
2	1	L-1512- MG

Components

#1: Protein

L RIBONUCLEASE E / / RNASE E

Details:

Mass: 58215.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

#2: RNA chain

R 5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP*UP*G)-3'

Details:

Mass: 4081.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

#3: Chemical

L-1510 L-1512 ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

#4: Chemical

L-1511 ChemComp-ZN / ZINC ION

Details:

Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

#5: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H₂O

• Compound details: MAJOR ENDORIBONUCLEASE PARTICIPATING IN MRNA TURNOVER IN E.COLI
• Sequence details: RESIDUES -6 TO 0 ARE FROM THE EXPRESSION SYSTEM.

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 6.6 ų/Da / Density % sol: 82 %
• Crystal grow: Temperature: 293 K / pH: 7.5 ; Details: CRYSTALS OF THE RNASE E CATALYTIC DOMAIN/ RNA COMPLEX APPEARED AFTER TWO TO FOUR WEEKS IN 5 TO 20 % WT/V POLYETHYLENE GLYCOL 8,000, 0.1 M TRIS PH 7.5 TO 8.0, AND 10 TO 50 MM MAGNESIUM FORMATE AT 20 C

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95
• Detector: Type: MARRESEARCH / Detector: CCD
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.95 Å / Relative weight: 1
• Reflection: Resolution: 3.2→25 Å / Num. obs: 27564 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 15.5 % / R_merge(I) obs: 0.11 / Net I/σ(I): 30
• Reflection shell: Resolution: 3.2→3.31 Å / Redundancy: 15 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 5.2 / % possible all: 96.7

Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BX2

2bx2

Resolution: 3.18→12 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.869 / SU B: 11.702 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.502 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE NOT INCLUDED IN THE MODEL. SOME SIDE CHAINS WERE TRUNCATED. SUGARS FOR CHAIN R AT POSITION 2 IS DISORDRED, WHILE THE BASES, SUGARS AND PHOSPHATES AT POSITIONS 3 AND 4 ARE ALSO DISORDERED. HOWEVER, ONE FEASIBLE CONFORMATION HAS BEEN INCLUDED IN THE MODEL.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.282	1349	5 %	RANDOM
Rwork	0.252	-	-	-
obs	0.254	25508	99.3 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 43.58 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.04 Å2	0.02 Å2	0 Å2
2-	-	0.04 Å2	0 Å2
3-	-	-	-0.06 Å2

Refinement step

Cycle: LAST / Resolution: 3.18→12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3555	214	3	49	3821

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	3859
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.583	2.04	5291
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.637	5	484
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.61	23.103	145
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.497	15	557
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.263	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.193	0.2	633
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2829
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.36	0.2	1993
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.354	0.2	2647
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.309	0.2	202
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.208	0.2	76
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.28	0.2	16
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.554	1.5	2459
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	7.194	2	3846
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	11.633	3	1538
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	15.488	4.5	1442
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.18→3.26 Å / Total num. of bins used: 20 /

	Rfactor	Num. reflection
Rfree	0.491	81
Rwork	0.357	1703