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- PDB-4okk: Crystal structure of RNase AS from M tuberculosis in complex with UMP -

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Basic information

Entry
Database: PDB / ID: 4okk
TitleCrystal structure of RNase AS from M tuberculosis in complex with UMP
Components3'-5' exoribonuclease Rv2179c/MT2234.1
KeywordsHYDROLASE / alpha/beta fold / exoribonuclease
Function / homology
Function and homology information


RNA exonuclease activity / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / magnesium ion binding / identical protein binding
Similarity search - Function
3-5 exoribonuclease, actinobacteria / 3'-5' exoribonuclease Rv2179c-like domain / 3'-5' exoribonuclease Rv2179c-like domain / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / 3'-5' exoribonuclease MT2234.1 / 3'-5' exoribonuclease Rv2179c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.21 Å
AuthorsRomano, M. / van de Weerd, R. / Brouwer, F.C.C. / Roviello, G.N. / Lacroix, R. / Sparrius, M. / van den Brink-van Stempvoort, G. / Maaskant, J.J. / van der Sar, A.M. / Appelmelk, B.J. ...Romano, M. / van de Weerd, R. / Brouwer, F.C.C. / Roviello, G.N. / Lacroix, R. / Sparrius, M. / van den Brink-van Stempvoort, G. / Maaskant, J.J. / van der Sar, A.M. / Appelmelk, B.J. / Geurtsen, J.J. / Berisio, R.
CitationJournal: Structure / Year: 2014
Title: Structure and Function of RNase AS, a Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence In Vivo
Authors: Romano, M. / van de Weerd, R. / Brouwer, F.C.C. / Roviello, G.N. / Lacroix, R. / Sparrius, M. / van den Brink-van Stempvoort, G. / Maaskant, J.J. / van der Sar, A.M. / Appelmelk, B.J. / ...Authors: Romano, M. / van de Weerd, R. / Brouwer, F.C.C. / Roviello, G.N. / Lacroix, R. / Sparrius, M. / van den Brink-van Stempvoort, G. / Maaskant, J.J. / van der Sar, A.M. / Appelmelk, B.J. / Geurtsen, J.J. / Berisio, R.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3'-5' exoribonuclease Rv2179c/MT2234.1
B: 3'-5' exoribonuclease Rv2179c/MT2234.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,82210
Polymers39,0282
Non-polymers7948
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-77 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.489, 76.848, 105.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3'-5' exoribonuclease Rv2179c/MT2234.1 / RNase AS


Mass: 19513.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2179c, MT2234.1 / Production host: Escherichia coli (E. coli)
References: UniProt: L7N5T0, UniProt: P9WJ73*PLUS, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 10%(w/v) polyethylene glycol 8000, 8%(v/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 9, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 18041 / Num. obs: 18023 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.24 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.21→14.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.239 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25876 848 5.1 %RANDOM
Rwork0.17951 ---
all0.1834 17050 --
obs0.1834 15731 92.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.21→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 46 338 3017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222761
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9693770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7345317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52821.806144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4215431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4151538
X-RAY DIFFRACTIONr_chiral_restr0.1150.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212168
X-RAY DIFFRACTIONr_mcbond_it1.1431.51603
X-RAY DIFFRACTIONr_mcangle_it2.07122613
X-RAY DIFFRACTIONr_scbond_it2.78731158
X-RAY DIFFRACTIONr_scangle_it4.5374.51157
LS refinement shellResolution: 2.205→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 71 -
Rwork0.261 1135 -
obs--93.42 %

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