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- PDB-2yjt: Crystal structure of E. coli DEAD-box protein SrmB bound to regul... -

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Basic information

Entry
Database: PDB / ID: 2yjt
TitleCrystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)
Components
  • ATP-DEPENDENT RNA HELICASE SRMB
  • REGULATOR OF RIBONUCLEASE ACTIVITY A
KeywordsHYDROLASE INHIBITOR/HYDROLASE / HYDROLASE INHIBITOR-HYDROLASE COMPLEX / DEAD BOX RNA HELICASES
Function / homology
Function and homology information


negative regulation of RNA catabolic process / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / ribonuclease inhibitor activity / oxaloacetate decarboxylase activity / RNA strand annealing activity / poly(A) binding / ATP-dependent activity, acting on RNA / protein homotrimerization / endoribonuclease inhibitor activity / ribosomal large subunit assembly ...negative regulation of RNA catabolic process / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / ribonuclease inhibitor activity / oxaloacetate decarboxylase activity / RNA strand annealing activity / poly(A) binding / ATP-dependent activity, acting on RNA / protein homotrimerization / endoribonuclease inhibitor activity / ribosomal large subunit assembly / RNA helicase activity / RNA helicase / enzyme binding / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP-dependent RNA helicase SrmB / Regulator of ribonuclease activity A, gammaproteobacteria / Regulator of ribonuclease activity A / Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site ...ATP-dependent RNA helicase SrmB / Regulator of ribonuclease activity A, gammaproteobacteria / Regulator of ribonuclease activity A / Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / 3-Layer(bba) Sandwich / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Regulator of ribonuclease activity A / ATP-dependent RNA helicase SrmB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPietras, Z. / Hardwick, S.W. / Luisi, B.F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Potential Regulatory Interactions of Escherichia Coli Rraa Protein with Dead-Box Helicases.
Authors: Pietras, Z. / Hardwick, S.W. / Swiezewski, S. / Luisi, B.F.
History
DepositionMay 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REGULATOR OF RIBONUCLEASE ACTIVITY A
B: REGULATOR OF RIBONUCLEASE ACTIVITY A
C: REGULATOR OF RIBONUCLEASE ACTIVITY A
D: ATP-DEPENDENT RNA HELICASE SRMB


Theoretical massNumber of molelcules
Total (without water)71,6734
Polymers71,6734
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-23.6 kcal/mol
Surface area33880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.390, 73.390, 222.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 2 - 159 / Label seq-ID: 2 - 159

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein REGULATOR OF RIBONUCLEASE ACTIVITY A / RRAA


Mass: 17371.264 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D8AM26, UniProt: P0A8R0*PLUS
#2: Protein ATP-DEPENDENT RNA HELICASE SRMB


Mass: 19559.531 Da / Num. of mol.: 1 / Fragment: RESIDUES 219-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21507, RNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.47 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD AT 16 DEG. C BY MIXING 1:1 PROTEIN SAMPLE WITH MOTHER LIQUOR: 100 MM MAGNESIUM ACETATE, 100 MM MOPS PH 7.2 AND 12% W/V PEG 8000.THE ...Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD AT 16 DEG. C BY MIXING 1:1 PROTEIN SAMPLE WITH MOTHER LIQUOR: 100 MM MAGNESIUM ACETATE, 100 MM MOPS PH 7.2 AND 12% W/V PEG 8000.THE CRYSTALS WERE TRANSFERRED BRIEFLY TO RESERVOIR SOLUTION SUPPLEMENTED WITH 25% (V/V) GLYCEROL AND FLASH FROZEN IN LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2010 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→63.56 Å / Num. obs: 15208 / % possible obs: 99.6 % / Observed criterion σ(I): 6 / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q5X

1q5x


Resolution: 2.9→74.3 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.882 / SU B: 16.027 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25658 804 5 %RANDOM
Rwork0.19227 ---
obs0.19544 15208 99.07 %-
Displacement parametersBiso mean: 39.431 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.48 Å20 Å2
2--0.97 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.9→74.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 0 29 4993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.591.966820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1245640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33424.286259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.39715832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7741544
X-RAY DIFFRACTIONr_chiral_restr0.1040.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023904
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6741.53157
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3125038
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74231883
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1074.51782
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

Ens-ID: 1 / Number: 1196 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.410.5
2Bmedium positional0.510.5
3Cmedium positional0.530.5
1Amedium thermal0.72
2Bmedium thermal0.682
3Cmedium thermal0.722
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 52 -
Rwork0.268 1082 -
obs--99.21 %

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