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- PDB-3r0p: Crystal structure of L-PSP putative endoribonuclease from uncultu... -

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Basic information

Entry
Database: PDB / ID: 3r0p
TitleCrystal structure of L-PSP putative endoribonuclease from uncultured organism
ComponentsL-PSP putative endoribonuclease
KeywordsHYDROLASE / endoribonuclease
Function / homology
Function and homology information


RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-PSP putative endoribonuclease
Similarity search - Component
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Petit, P. / Xu, X. / Cui, H. / Savchenko, A. / Yakunin, A.F.
CitationJournal: To be Published
Title: Crystal structure of L-PSP putative endoribonuclease from uncultured organism
Authors: Cuff, M.E. / Petit, P. / Xu, X. / Cui, H. / Savchenko, A. / Yakunin, A.F.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-PSP putative endoribonuclease
B: L-PSP putative endoribonuclease
C: L-PSP putative endoribonuclease
D: L-PSP putative endoribonuclease
E: L-PSP putative endoribonuclease
F: L-PSP putative endoribonuclease


Theoretical massNumber of molelcules
Total (without water)81,9106
Polymers81,9106
Non-polymers00
Water7,350408
1
A: L-PSP putative endoribonuclease
B: L-PSP putative endoribonuclease
F: L-PSP putative endoribonuclease


Theoretical massNumber of molelcules
Total (without water)40,9553
Polymers40,9553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-22 kcal/mol
Surface area14150 Å2
MethodPISA
2
C: L-PSP putative endoribonuclease
D: L-PSP putative endoribonuclease
E: L-PSP putative endoribonuclease


Theoretical massNumber of molelcules
Total (without water)40,9553
Polymers40,9553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-27 kcal/mol
Surface area14460 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-61 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.414, 82.680, 99.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-PSP putative endoribonuclease


Mass: 13651.667 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D8VN48
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 0.2M Ammonium sulphate, 25% PEG3350, 1/75 subtilisin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 54073 / Num. obs: 42525 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2647 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.532 Å / SU ML: 0.24 / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 4982 5.1 %RANDOM
Rwork0.1767 ---
obs0.1786 -94.55 %-
all-51672 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.04 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.776 Å2-0 Å2-0 Å2
2---12.8388 Å20 Å2
3----4.9372 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5638 0 0 408 6046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065740
X-RAY DIFFRACTIONf_angle_d1.0567832
X-RAY DIFFRACTIONf_dihedral_angle_d11.3912056
X-RAY DIFFRACTIONf_chiral_restr0.072929
X-RAY DIFFRACTIONf_plane_restr0.0051031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9004-1.96830.30444600.2548067X-RAY DIFFRACTION82
1.9683-2.04710.24815050.21338647X-RAY DIFFRACTION89
2.0471-2.14030.26734270.19738980X-RAY DIFFRACTION91
2.1403-2.25320.25924770.18939286X-RAY DIFFRACTION94
2.2532-2.39430.26594920.18769354X-RAY DIFFRACTION96
2.3943-2.57920.24495200.19519466X-RAY DIFFRACTION97
2.5792-2.83870.21215030.18039703X-RAY DIFFRACTION99
2.8387-3.24930.23175170.1999713X-RAY DIFFRACTION99
3.2493-4.09320.18195330.15899741X-RAY DIFFRACTION100
4.0932-42.54260.16455480.14489722X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.2817 Å / Origin y: 20.9272 Å / Origin z: 53.1229 Å
111213212223313233
T0.1186 Å20.0147 Å2-0.0258 Å2-0.1528 Å2-0.0028 Å2--0.1461 Å2
L0.0658 °20.03 °2-0.0465 °2-1.8564 °21.3965 °2--1.3217 °2
S0.0176 Å °-0.0085 Å °-0.0132 Å °0.2474 Å °0.0145 Å °-0.0839 Å °0.2447 Å °0.0221 Å °-0.032 Å °
Refinement TLS groupSelection details: all

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