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- PDB-4haa: Structure of Ribonuclease Binase Glu43Ala/Phe81Ala Mutant -

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Basic information

Entry
Database: PDB / ID: 4haa
TitleStructure of Ribonuclease Binase Glu43Ala/Phe81Ala Mutant
ComponentsRibonuclease
KeywordsHYDROLASE / endoribonuclease
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus intermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPolyakov, K.M. / Trofimov, A.A. / Mitchevich, V.A. / Dorovatovskii, P.V. / Schulga, A.A. / Makarov, A.A. / Tkach, E.N. / Goncharuk, D.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure and functional studies of the ribonuclease binase Glu43Ala/Phe81Ala mutant.
Authors: Mitkevich, V.A. / Schulga, A.A. / Trofimov, A.A. / Dorovatovskii, P.V. / Goncharuk, D.A. / Tkach, E.N. / Makarov, A.A. / Polyakov, K.M.
History
DepositionSep 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease
B: Ribonuclease
C: Ribonuclease
D: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)48,3744
Polymers48,3744
Non-polymers00
Water4,756264
1
A: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)12,0931
Polymers12,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)12,0931
Polymers12,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)12,0931
Polymers12,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)12,0931
Polymers12,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.360, 50.360, 196.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Ribonuclease / Binase / RNase Bi


Mass: 12093.490 Da / Num. of mol.: 4 / Fragment: UNP residues 54-162 / Mutation: E43A/F81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus intermedius (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P00649, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 10 mg/mL protein, reservoir: 0.1 M citric acid, pH 3.5, 3 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.983 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.524
11-H, K, -L20.476
ReflectionResolution: 1.89→60 Å / Num. all: 37967 / Num. obs: 37967 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091
Reflection shellResolution: 1.89→2.01 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.49 / Num. unique all: 5895 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOV

1gov


Resolution: 1.9→18.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.02 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20544 1909 5 %RANDOM
Rwork0.17714 ---
obs0.1786 35961 98.95 %-
all-35961 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.062 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--2.06 Å20 Å2
3----4.12 Å2
Refine analyzeLuzzati coordinate error free: 0.027 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 0 264 3688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193500
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9324752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5915432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.80121.707164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06315544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0161540
X-RAY DIFFRACTIONr_chiral_restr0.1230.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212716
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 133 -
Rwork0.214 2535 -
obs--94.18 %

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