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- PDB-7va6: PaOrn Oligoribonuclease D11A mutant with RNA GU complex structure -

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Basic information

Entry
Database: PDB / ID: 7va6
TitlePaOrn Oligoribonuclease D11A mutant with RNA GU complex structure
Components
  • Oligoribonuclease
  • RNA (5'-R(P*GP*U)-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 / DNA metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / 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
IMIDAZOLE / RNA / Oligoribonuclease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 RNA GU 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 1.2Nov 6, 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: Oligoribonuclease
B: Oligoribonuclease
C: RNA (5'-R(P*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2954
Polymers42,2263
Non-polymers691
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-20 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.993, 82.993, 192.923
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*U)-3')


Mass: 606.414 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.93 Å3/Da / Density % sol: 68.67 %
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: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38215 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 40.3 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.056 / Net I/σ(I): 22.74
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.44 / Num. unique obs: 1918 / CC1/2: 0.884 / CC star: 0.969 / Rpim(I) all: 0.296 / % possible all: 99.9

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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: 2.1→26.75 Å / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.5548
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196 2002 5.25 %
Rwork0.1665 36146 -
obs0.168 38148 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 43 5 227 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672976
X-RAY DIFFRACTIONf_angle_d0.75084041
X-RAY DIFFRACTIONf_chiral_restr0.0505447
X-RAY DIFFRACTIONf_plane_restr0.0047522
X-RAY DIFFRACTIONf_dihedral_angle_d14.0378409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.25521360.21882501X-RAY DIFFRACTION97.2
2.14-2.20.22111450.20682582X-RAY DIFFRACTION99.96
2.2-2.270.26031430.19132586X-RAY DIFFRACTION99.85
2.27-2.340.241420.18262568X-RAY DIFFRACTION99.93
2.34-2.420.21231370.17382569X-RAY DIFFRACTION99.85
2.42-2.520.21211440.18442607X-RAY DIFFRACTION99.93
2.52-2.640.25651440.18862574X-RAY DIFFRACTION99.89
2.64-2.770.24041440.19342585X-RAY DIFFRACTION99.89
2.77-2.950.25661410.18642604X-RAY DIFFRACTION99.96
2.95-3.180.22681460.19512572X-RAY DIFFRACTION99.96
3.18-3.490.20611430.17252592X-RAY DIFFRACTION99.93
3.49-40.20061440.15092590X-RAY DIFFRACTION100
4-5.030.13281420.13592598X-RAY DIFFRACTION99.85
5.03-26.750.16441510.15422618X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 14.8436713698 Å / Origin y: 34.4930972323 Å / Origin z: 0.582764093265 Å
111213212223313233
T0.228084394304 Å2-0.0140601105335 Å2-0.00144402762546 Å2-0.383347665999 Å2-0.00871801812509 Å2--0.330367973552 Å2
L0.313095696643 °20.126897517613 °20.486803146193 °2-1.03844684448 °20.888530566384 °2--1.60595517957 °2
S-0.0394554962294 Å °0.121770220471 Å °-0.0143496736408 Å °0.0601981052669 Å °0.0306736418239 Å °-0.125136176364 Å °0.122411174602 Å °0.165339161252 Å °3.20107806943E-6 Å °
Refinement TLS groupSelection details: all

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