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- PDB-6x2d: Crystal Structure of DNase I Domain of Ribonuclease E from Vibrio... -

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Basic information

Entry
Database: PDB / ID: 6x2d
TitleCrystal Structure of DNase I Domain of Ribonuclease E from Vibrio cholerae
ComponentsRibonuclease E
KeywordsRNA BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding ...ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
: / 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
Similarity search - Domain/homology
IODIDE ION / Ribonuclease E
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of DNase I Domain of Ribonuclease E from Vibrio cholerae.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease E
B: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8379
Polymers25,9492
Non-polymers8887
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-13 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.614, 58.812, 47.046
Angle α, β, γ (deg.)90.000, 108.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease E / RNase E


Mass: 12974.358 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: rne, VC_2030 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): (DE3)magic / References: UniProt: Q9KQG8, ribonuclease E
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 7.9 mg/ml, 0.01M Tris pH 8.3; Screen: PACT (F3), 0.2M Sodium iodide, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2020 / Details: Be
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 17863 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.041 / Rrim(I) all: 0.097 / Rsym value: 0.088 / Χ2: 1.466 / Net I/σ(I): 21.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 897 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.339 / Rrim(I) all: 0.833 / Rsym value: 0.759 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vrt

2vrt


Resolution: 1.85→29.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.97 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 887 5 %RANDOM
Rwork0.2067 ---
obs0.2085 16959 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.88 Å2 / Biso mean: 43.735 Å2 / Biso min: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å21.64 Å2
2---1.57 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 1.85→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 9 75 1793
Biso mean--80.56 48.64 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171716
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.6522336
X-RAY DIFFRACTIONr_angle_other_deg0.411.5853933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0495217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.20419.28125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.08415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4341532
X-RAY DIFFRACTIONr_chiral_restr0.0570.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.050.021977
X-RAY DIFFRACTIONr_gen_planes_other0.0440.02395
LS refinement shellResolution: 1.852→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 67 -
Rwork0.249 1168 -
all-1235 -
obs--93.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7316-0.0183-2.2391.1708-0.47271.6657-0.1995-0.11530.06-0.03370.0769-0.12480.32780.03890.12260.31410.00450.1650.0082-0.00950.10383.543-1.871-3.557
21.60880.1813-0.88840.99460.39931.5445-0.05860.0853-0.0696-0.0947-0.0033-0.15950.0411-0.06750.06190.23660.00540.11670.03270.00090.07882.0756.76-6.358
32.45060.47021.34960.10180.05125.116-0.03710.09580.0638-0.01420.03150.0034-0.0247-0.18420.00560.21650.00890.08870.07370.00380.0759-5.97510.595-6.351
41.8539-1.854-1.15012.17571.9452.7566-0.15770.1976-0.29120.3887-0.21280.32850.7945-0.20060.37050.3859-0.08820.21320.0444-0.07430.1814-16.032-1.32713.141
51.7194-2.0084-1.01262.78940.21782.8222-0.20510.0359-0.15440.22980.03940.19840.1926-0.11690.16570.1885-0.01680.12050.06760.0460.1439-14.258.3916.7
61.1362-1.58630.33072.2294-0.64174.0944-0.1252-0.0865-0.01510.19050.12650.03650.11440.2925-0.00120.20510.02710.10010.11560.01780.0608-3.9678.53217.06
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 317
2X-RAY DIFFRACTION2A318 - 361
3X-RAY DIFFRACTION3A362 - 390
4X-RAY DIFFRACTION4B279 - 312
5X-RAY DIFFRACTION5B313 - 361
6X-RAY DIFFRACTION6B362 - 390

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