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- PDB-7va2: PaOrn Oligoribonuclease D11A mutant with product GMP complex structure -

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Basic information

Entry
Database: PDB / ID: 7va2
TitlePaOrn Oligoribonuclease D11A mutant with product GMP complex structure
ComponentsOligoribonuclease
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
GUANOSINE-5'-MONOPHOSPHATE / IMIDAZOLE / PHOSPHATE ION / Oligoribonuclease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 product GMP 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 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1465
Polymers41,6192
Non-polymers5273
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-23 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.627, 82.627, 192.577
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: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.94 Å3/Da / Density % sol: 68.79 %
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: 2.3→50 Å / Num. obs: 30350 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.05 Å2 / CC1/2: 0.969 / CC star: 0.992 / Rpim(I) all: 0.092 / Net I/σ(I): 15.61
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 1541 / CC1/2: 0.701 / CC star: 0.908 / % possible all: 100

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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: 2.3→34.91 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 2011 6.65 %
Rwork0.1939 28214 -
obs0.1965 30225 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 34 84 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713021
X-RAY DIFFRACTIONf_angle_d0.88914098
X-RAY DIFFRACTIONf_chiral_restr0.051447
X-RAY DIFFRACTIONf_plane_restr0.0055533
X-RAY DIFFRACTIONf_dihedral_angle_d21.6479407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.31161430.26932003X-RAY DIFFRACTION98.94
2.37-2.440.29251470.2392038X-RAY DIFFRACTION99.86
2.44-2.510.28121440.24582000X-RAY DIFFRACTION99.31
2.51-2.60.29061480.2362032X-RAY DIFFRACTION99.86
2.6-2.710.28061430.24032028X-RAY DIFFRACTION99.68
2.71-2.830.26061450.22492029X-RAY DIFFRACTION99.63
2.83-2.980.28691430.23732019X-RAY DIFFRACTION99.95
2.98-3.170.30781450.23022064X-RAY DIFFRACTION100
3.17-3.410.24281460.20792030X-RAY DIFFRACTION99.86
3.41-3.750.23891450.19452039X-RAY DIFFRACTION99.64
3.76-4.30.23211420.16652019X-RAY DIFFRACTION99.49
4.3-5.410.17411420.15272050X-RAY DIFFRACTION99.77
5.41-34.910.18851440.17172037X-RAY DIFFRACTION99.05
Refinement TLS params.Method: refined / Origin x: 97.8144293403 Å / Origin y: 89.5912685673 Å / Origin z: 0.910304144951 Å
111213212223313233
T0.321827031674 Å20.0225873075718 Å20.00261152013301 Å2-0.491977041594 Å2-0.005197072087 Å2--0.403931941379 Å2
L0.318172220616 °20.051099275554 °2-0.365412871098 °2-0.749162219783 °20.648125083142 °2--1.13479686001 °2
S-0.0613580459758 Å °-0.127871127566 Å °-0.00867481912775 Å °-0.0631793969871 Å °0.0292671118759 Å °-0.0655046249341 Å °-0.117665004779 Å °0.163328316175 Å °-6.92345999722E-5 Å °
Refinement TLS groupSelection details: all

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