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- PDB-3dd6: Crystal structure of Rph, an exoribonuclease from Bacillus anthra... -

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Basic information

Entry
Database: PDB / ID: 3dd6
TitleCrystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution
ComponentsRibonuclease PH
KeywordsTRANSFERASE / Exoribonuclease / Bacillus anthracis / tRNA maturation / RNase Ph. / Structural Genomics / Structural Proteomics in Europe 2 / SPINE-2
Function / homology
Function and homology information


tRNA nucleotidyltransferase / tRNA nucleotidyltransferase activity / rRNA catabolic process / tRNA processing / RNA nuclease activity / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding
Similarity search - Function
Ribonuclease PH, bacterial-type / Ribonuclease PH, conserved site / Ribonuclease PH signature. / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 ...Ribonuclease PH, bacterial-type / Ribonuclease PH, conserved site / Ribonuclease PH signature. / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsRawlings, A.E. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Wilson, K.S. / Wilkinson, A.J. / Structural Proteomics in Europe 2 (SPINE-2)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 A resolution.
Authors: Rawlings, A.E. / Blagova, E.V. / Levdikov, V.M. / Fogg, M.J. / Wilson, K.S. / Wilkinson, A.J.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Structure summary
Category: audit_author / pdbx_database_related ...audit_author / pdbx_database_related / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_keywords
Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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 / _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: Ribonuclease PH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6876
Polymers28,2071
Non-polymers4805
Water2,594144
1
A: Ribonuclease PH
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)172,12436
Polymers169,2436
Non-polymers2,88230
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area24560 Å2
ΔGint-496 kcal/mol
Surface area56930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.750, 86.750, 179.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

21A-615-

HOH

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Components

#1: Protein Ribonuclease PH / E.C.2.7.7.56 / RNase PH / tRNA nucleotidyltransferase


Mass: 28207.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: Rph / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q81LA9, tRNA nucleotidyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulphate, K/Na tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→43.36 Å / Num. all: 28380 / Num. obs: 28380 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 27.43 Å2 / Rsym value: 0.04 / Net I/σ(I): 25.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 3948 / Rsym value: 0.38 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.4refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYR

1oyr


Resolution: 1.702→34.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.834 / SU ML: 0.094 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.24414 1413 5 %RANDOM
Rwork0.21227 ---
obs0.21384 26895 98.42 %-
all-26895 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.643 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.14 Å20 Å2
2---0.27 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.702→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 25 144 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221931
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9752613
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6315248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69924.33783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64615351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5231515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021412
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_it0.761.51216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24621958
X-RAY DIFFRACTIONr_scbond_it2.2353715
X-RAY DIFFRACTIONr_scangle_it3.4994.5654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 81 -
Rwork0.3 1852 -
obs-1413 92.75 %
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)
12.81910.7353-4.07023.8236-0.2886.04110.46920.20560.1495-0.5351-0.41210.0104-0.21750.5088-0.05710.13490.0241-0.0935-0.0682-0.04230.22641.8606-5.385-18.8243
22.1578-0.04710.25531.9228-0.46731.4663-0.15360.3830.3588-0.18770.04420.08560.06750.10880.1094-0.0935-0.0216-0.0376-0.05340.0795-0.1563.2219-23.9341-40.1695
315.3988-0.27235.58594.80810.376414.40980.20460.2308-1.2823-0.0826-0.28021.22010.7501-0.42070.07560.1772-0.1524-0.03060.1302-0.06740.0503-6.7343-35.1039-53.2185
46.6308-1.39122.32190.5165-0.73841.0941-0.0812-0.0461-0.31870.35970.10670.42930.08440.0688-0.02550.10140.02830.02130.02610.0035-0.09654.8179-34.7273-22.751
52.7618-0.5116-1.0922.620.75372.202-0.00760.40580.6975-0.22920.02730.2235-0.3367-0.0276-0.0197-0.0337-0.0162-0.0968-0.07990.13610.1015-0.7878-10.9584-41.2868
62.97310.8649-0.93332.2401-0.24730.73060.1201-0.30680.73420.4484-0.07080.50150.0236-0.119-0.04930.03740.04210.064-0.0987-0.07780.2211-11.9582-16.1484-23.6883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1311 - 23
2X-RAY DIFFRACTION2AA14 - 4624 - 56
3X-RAY DIFFRACTION2AA57 - 6467 - 74
4X-RAY DIFFRACTION2AA87 - 15197 - 161
5X-RAY DIFFRACTION3AA47 - 5657 - 66
6X-RAY DIFFRACTION4AA65 - 8675 - 96
7X-RAY DIFFRACTION5AA152 - 163162 - 173
8X-RAY DIFFRACTION5AA223 - 245233 - 255
9X-RAY DIFFRACTION6AA164 - 187174 - 197
10X-RAY DIFFRACTION6AA188 - 203198 - 213
11X-RAY DIFFRACTION6AA204 - 222214 - 232

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