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- PDB-2vmk: Crystal Structure of E. coli RNase E Apoprotein - Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 2vmk
TitleCrystal Structure of E. coli RNase E Apoprotein - Catalytic Domain
ComponentsRIBONUCLEASE E
KeywordsHYDROLASE / NUCLEASE / CYTOPLASM / RNA-BINDING / RNA TURNOVER / ENDONUCLEASE / RNA PROCESSING
Function / homology
Function and homology information


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 ...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 / molecular adaptor activity / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKoslover, D.J. / Callaghan, A.J. / Marcaida, M.J. / Martick, M. / Scott, W.G. / Luisi, B.F.
CitationJournal: Structure / Year: 2008
Title: The Crystal Structure of the Escherichia Coli Rnase E Apoprotein and a Mechanism for RNA Degradation.
Authors: Koslover, D.J. / Callaghan, A.J. / Marcaida, M.J. / Garman, E.F. / Martick, M. / Scott, W.G. / Luisi, B.F.
History
DepositionJan 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)232,0549
Polymers231,6354
Non-polymers4195
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16440 Å2
ΔGint-90.4 kcal/mol
Surface area107090 Å2
MethodPQS
Unit cell
Length a, b, c (Å)73.241, 75.571, 109.370
Angle α, β, γ (deg.)94.95, 102.03, 91.77
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 212
2111B1 - 212
3111C1 - 212
4111D1 - 212
1121A213 - 400
2121B213 - 400
3121C213 - 400
4121D213 - 400
1131A420 - 500
2131B420 - 500
3131C420 - 500
4131D420 - 500

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
RIBONUCLEASE E / / RNASE E


Mass: 57908.789 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET16B VARIANT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.89 Å3/Da / Density % sol: 44.2 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.28
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 3.22→50 Å / Num. obs: 34917 / % possible obs: 91.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.1
Reflection shellResolution: 3.22→3.34 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.7 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
MOLREPphasing
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BX2

2bx2


Resolution: 3.3→47.84 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / ESU R Free: 0.666 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1664 5 %RANDOM
Rwork0.267 ---
obs0.268 31611 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.52 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å2-6.28 Å2-1.94 Å2
2---1.95 Å20.41 Å2
3----3.73 Å2
Refinement stepCycle: LAST / Resolution: 3.3→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14170 0 17 0 14187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02114394
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.951.9719588
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.59551903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63823.536577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.652152208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.19415114
X-RAY DIFFRACTIONr_chiral_restr0.1110.22354
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0210830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.36329
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.39867
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.5792
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5570.387
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5180.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.20429605
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6315221
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.70824789
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.4234367
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1138tight positional0.360.03
12B1138tight positional0.30.03
13C1138tight positional0.320.03
14D1138tight positional0.260.03
21A1231tight positional0.320.03
22B1231tight positional0.240.03
23C1231tight positional0.440.03
24D1231tight positional0.180.03
31A588tight positional0.150.03
32B588tight positional0.210.03
33C588tight positional0.130.03
34D588tight positional0.130.03
11A1138tight thermal1.790.2
12B1138tight thermal2.080.2
13C1138tight thermal2.280.2
14D1138tight thermal4.280.2
21A1231tight thermal1.750.2
22B1231tight thermal1.320.2
23C1231tight thermal2.040.2
24D1231tight thermal2.220.2
31A588tight thermal2.040.2
32B588tight thermal1.790.2
33C588tight thermal0.510.2
34D588tight thermal0.530.2
LS refinement shellResolution: 3.3→3.38 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 132
Rwork0.346 2194

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