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- PDB-7va3: PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex s... -

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Basic information

Entry
Database: PDB / ID: 7va3
TitlePaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure
Components
  • Oligoribonuclease
  • RNA (5'-R(P*GP*G)-3')
KeywordsHYDROLASE / PaOrn / Oligoribonuclease / Pseudomonas aeruginosa.
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
IMIDAZOLE / : / RNA / Oligoribonuclease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, J. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: To Be Published
Title: PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure
Authors: Zhang, J. / Zhang, Q. / Bartlam, M.
History
DepositionAug 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: Oligoribonuclease
B: Oligoribonuclease
C: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4446
Polymers42,2653
Non-polymers1793
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-24 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.223, 83.223, 192.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Oligoribonuclease


Mass: 20809.586 Da / Num. of mol.: 2 / Mutation: D11A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: orn, PA4951 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P57665, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*GP*G)-3')


Mass: 645.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.01 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 1.2M (NH4)2HPO4, 0.1M imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 60258 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.95 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rpim(I) all: 0.072 / Net I/σ(I): 28.44
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 2938 / CC1/2: 0.889 / CC star: 0.97 / Rpim(I) all: 0.343 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V9Z

7v9z


Resolution: 1.8→41.61 Å / SU ML: 0.1893 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.0385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1912 1990 3.33 %
Rwork0.1722 57847 -
obs0.1728 59837 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 46 7 261 3222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063029
X-RAY DIFFRACTIONf_angle_d0.69664111
X-RAY DIFFRACTIONf_chiral_restr0.0491452
X-RAY DIFFRACTIONf_plane_restr0.004530
X-RAY DIFFRACTIONf_dihedral_angle_d10.5583416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.35531380.32123960X-RAY DIFFRACTION95.44
1.84-1.890.27281370.28164094X-RAY DIFFRACTION98.33
1.89-1.950.27931440.25794098X-RAY DIFFRACTION98.7
1.95-2.010.25481440.22084149X-RAY DIFFRACTION99.19
2.01-2.080.22231420.20554112X-RAY DIFFRACTION98.72
2.08-2.170.23181390.18154111X-RAY DIFFRACTION99.09
2.17-2.270.19321390.17224162X-RAY DIFFRACTION99.56
2.27-2.390.18491430.15994133X-RAY DIFFRACTION99.53
2.39-2.540.20731430.17544138X-RAY DIFFRACTION99.51
2.54-2.730.20861470.18794150X-RAY DIFFRACTION99.68
2.73-3.010.22431430.1894183X-RAY DIFFRACTION99.98
3.01-3.440.18521430.17924174X-RAY DIFFRACTION99.86
3.44-4.330.17151390.14934181X-RAY DIFFRACTION99.86
4.33-41.610.15291490.14374202X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: 98.2861596772 Å / Origin y: 90.2662475624 Å / Origin z: 0.608556834383 Å
111213212223313233
T0.247876829834 Å20.00677061325956 Å20.00240258337392 Å2-0.430681955577 Å20.0051420553413 Å2--0.301564374222 Å2
L0.576115374318 °2-0.153762279163 °2-0.492462169122 °2-1.27618269335 °21.02370844584 °2--2.12238092992 °2
S-0.0698691679013 Å °-0.178058061346 Å °-0.00206859964223 Å °-0.0274827491243 Å °0.044107362159 Å °-0.146238222268 Å °-0.123000926319 Å °0.245998460912 Å °0.0418944881472 Å °
Refinement TLS groupSelection details: ALL

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