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- PDB-2yjv: Crystal structure of E. coli regulator of ribonuclease activity A... -

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Basic information

Entry
Database: PDB / ID: 2yjv
TitleCrystal structure of E. coli regulator of ribonuclease activity A (RraA) bound to fragment of DEAD-box protein RhlB
Components
  • ATP-DEPENDENT RNA HELICASE RHLB
  • 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 / protein homotrimerization / endoribonuclease inhibitor activity / enzyme binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
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 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulator of ribonuclease activity A
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 24, 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 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: REGULATOR OF RIBONUCLEASE ACTIVITY A
E: REGULATOR OF RIBONUCLEASE ACTIVITY A
F: REGULATOR OF RIBONUCLEASE ACTIVITY A
G: REGULATOR OF RIBONUCLEASE ACTIVITY A
H: REGULATOR OF RIBONUCLEASE ACTIVITY A
I: REGULATOR OF RIBONUCLEASE ACTIVITY A
J: REGULATOR OF RIBONUCLEASE ACTIVITY A
K: REGULATOR OF RIBONUCLEASE ACTIVITY A
L: REGULATOR OF RIBONUCLEASE ACTIVITY A
M: ATP-DEPENDENT RNA HELICASE RHLB
N: ATP-DEPENDENT RNA HELICASE RHLB


Theoretical massNumber of molelcules
Total (without water)210,02314
Polymers210,02314
Non-polymers00
Water1,17165
1
A: REGULATOR OF RIBONUCLEASE ACTIVITY A
B: REGULATOR OF RIBONUCLEASE ACTIVITY A
C: REGULATOR OF RIBONUCLEASE ACTIVITY A


Theoretical massNumber of molelcules
Total (without water)52,1143
Polymers52,1143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-16.2 kcal/mol
Surface area19510 Å2
MethodPISA
2
D: REGULATOR OF RIBONUCLEASE ACTIVITY A
E: REGULATOR OF RIBONUCLEASE ACTIVITY A
F: REGULATOR OF RIBONUCLEASE ACTIVITY A


Theoretical massNumber of molelcules
Total (without water)52,1143
Polymers52,1143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-16.6 kcal/mol
Surface area19470 Å2
MethodPISA
3
G: REGULATOR OF RIBONUCLEASE ACTIVITY A
H: REGULATOR OF RIBONUCLEASE ACTIVITY A
I: REGULATOR OF RIBONUCLEASE ACTIVITY A


Theoretical massNumber of molelcules
Total (without water)52,1143
Polymers52,1143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-16.2 kcal/mol
Surface area19570 Å2
MethodPISA
4
J: REGULATOR OF RIBONUCLEASE ACTIVITY A
K: REGULATOR OF RIBONUCLEASE ACTIVITY A
L: REGULATOR OF RIBONUCLEASE ACTIVITY A


Theoretical massNumber of molelcules
Total (without water)52,1143
Polymers52,1143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-15.4 kcal/mol
Surface area19570 Å2
MethodPISA
5
M: ATP-DEPENDENT RNA HELICASE RHLB


  • defined by author&software
  • 784 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7841
Polymers7841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
N: ATP-DEPENDENT RNA HELICASE RHLB


  • defined by author&software
  • 784 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7841
Polymers7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)259.630, 69.070, 123.300
Angle α, β, γ (deg.)90.00, 109.17, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 157
2114B2 - 157
3114C2 - 157
4114D2 - 157
5114E2 - 157
6114F2 - 157
7114G2 - 157
8114H2 - 157
9114I2 - 157
10114J2 - 157
11114K2 - 157
12114L2 - 157

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Components

#1: Protein
REGULATOR OF RIBONUCLEASE ACTIVITY A / RRAA


Mass: 17371.264 Da / Num. of mol.: 12
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: P0A8R0
#2: Protein/peptide ATP-DEPENDENT RNA HELICASE RHLB / RHLB


Mass: 783.958 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: DNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS M AND N ARE PEPTIDE OF SEQUENCE YRLTRPRTGNGPRRTGAPRNRRRSG WHICH CORRESPONDS TO RESIDUES 398- ...CHAINS M AND N ARE PEPTIDE OF SEQUENCE YRLTRPRTGNGPRRTGAPRNRRRSG WHICH CORRESPONDS TO RESIDUES 398-421 OF RHLB (UNIPROT P0A8J8) WITH AN ADDED N-TERMINAL TYROSINE RESIDUE, TO ENABLE ESTIMATION OF PEPTIDE CONCENTRATION BY UV ABSORPTION

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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: 2.58 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: CRYSTALS WERE OBTAINED USING THE HANGING DROP METHOD, BY MIXING IN 1 TO 1 RATIO PROTEIN SAMPLE WITH MOTHER LIQUOR 100 MM SODIUM CITRATE PH 5.4, 32% MPD AND 200 MM AMMONIUM ACETATE AT 25 C. ...Details: CRYSTALS WERE OBTAINED USING THE HANGING DROP METHOD, BY MIXING IN 1 TO 1 RATIO PROTEIN SAMPLE WITH MOTHER LIQUOR 100 MM SODIUM CITRATE PH 5.4, 32% MPD AND 200 MM AMMONIUM ACETATE AT 25 C. PLATES WERE THEN IMMEDIATELY TRANSFERRED TO 16 C. CRYSTALS WERE DIRECTLY FLASH FROZEN IN LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 7, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→63.53 Å / Num. obs: 47500 / % possible obs: 98 % / Observed criterion σ(I): 6 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3

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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: 2.8→122.62 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / SU B: 19.997 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28774 2535 5.1 %RANDOM
Rwork0.22087 ---
obs0.22434 47500 97.52 %-
Displacement parametersBiso mean: 57.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å21.25 Å2
2--2.63 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→122.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14380 0 0 65 14445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02214597
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.96219783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61951893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47225.213752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.141152288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.071596
X-RAY DIFFRACTIONr_chiral_restr0.10.22219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211408
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_it0.6951.59305
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.226214779
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64735292
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0034.55004
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: 1180 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.440.5
2Bmedium positional0.40.5
3Cmedium positional0.370.5
4Dmedium positional0.430.5
5Emedium positional0.350.5
6Fmedium positional0.410.5
7Gmedium positional0.370.5
8Hmedium positional0.40.5
9Imedium positional0.410.5
10Jmedium positional0.380.5
11Kmedium positional0.450.5
12Lmedium positional0.720.5
1Amedium thermal0.952
2Bmedium thermal0.832
3Cmedium thermal1.342
4Dmedium thermal0.612
5Emedium thermal0.742
6Fmedium thermal1.62
7Gmedium thermal0.882
8Hmedium thermal0.82
9Imedium thermal0.662
10Jmedium thermal0.852
11Kmedium thermal1.142
12Lmedium thermal1.912
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 185 -
Rwork0.363 3527 -
obs--99.07 %

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