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- PDB-7xgt: Crystal structure of rice OsRNase ZS1 -

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Basic information

Entry
Database: PDB / ID: 7xgt
TitleCrystal structure of rice OsRNase ZS1
ComponentsRNase ZS1
KeywordsRNA BINDING PROTEIN / RNase ZS1 / tRNA repair / Zinc
Function / homologyBeta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta / Nuclear ribonuclease Z
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMao, Y. / Gao, F. / Chen, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509903 China
CitationJournal: To Be Published
Title: Crystal structure of rice OsRNase ZS1
Authors: Mao, Y. / Gao, F. / Chen, Y.H.
History
DepositionApr 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNase ZS1
B: RNase ZS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4898
Polymers67,1032
Non-polymers3866
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-173 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.368, 83.148, 87.147
Angle α, β, γ (deg.)90.000, 109.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

21A-640-

HOH

31B-571-

HOH

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Components

#1: Protein RNase ZS1 / Putative nuclear ribonuclease Z


Mass: 33551.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0VGC7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 3350, 100 mM Na-citrate pH 5.5, 100 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.7→32.952 Å / Num. obs: 64632 / % possible obs: 98.92 % / Redundancy: 15.2 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.022 / Rrim(I) all: 0.088 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 15 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6404 / CC1/2: 0.778 / CC star: 0.935 / Rpim(I) all: 0.362 / % possible all: 98.98

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→32.952 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 3175 4.91 %
Rwork0.1723 61457 -
obs0.1736 64632 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.08 Å2 / Biso mean: 38.046 Å2 / Biso min: 13.8 Å2
Refinement stepCycle: final / Resolution: 1.7→32.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 12 215 4547
Biso mean--60.9 38.15 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72490.30831570.2925263098
1.7249-1.75180.31821270.2707263299
1.7518-1.78060.29231470.2556268399
1.7806-1.81130.27311400.2431261698
1.8113-1.84420.2361270.2202267499
1.8442-1.87970.22521380.2068268399
1.8797-1.9180.24011300.1946264899
1.918-1.95970.23631420.1904269799
1.9597-2.00530.21141330.176268199
2.0053-2.05540.2061600.1777261199
2.0554-2.1110.22011580.1816268099
2.111-2.17310.23331410.1745263398
2.1731-2.24320.20131300.1675270199
2.2432-2.32340.21461380.15812670100
2.3234-2.41640.21081170.1723269599
2.4164-2.52630.20081230.1645271099
2.5263-2.65950.18341420.1638265499
2.6595-2.8260.18621360.1701263397
2.826-3.04410.2121360.1737268899
3.0441-3.35010.181350.17392709100
3.3501-3.83430.19841420.1622269299
3.8343-4.82830.16181410.1402269699
4.8283-32.9520.19541350.1719274198

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