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- PDB-3tsr: X-ray structure of mouse ribonuclease inhibitor complexed with mo... -

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Basic information

Entry
Database: PDB / ID: 3tsr
TitleX-ray structure of mouse ribonuclease inhibitor complexed with mouse ribonuclease 1
Components
  • Ribonuclease inhibitor
  • Ribonuclease pancreatic
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / hydrolase inhibitor / leucine-rich repeat / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / ribonuclease inhibitor activity / angiogenin-PRI complex / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / regulation of angiogenesis / response to bacterium / nucleic acid binding / lyase activity ...: / ribonuclease inhibitor activity / angiogenin-PRI complex / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / regulation of angiogenesis / response to bacterium / nucleic acid binding / lyase activity / extracellular region / nucleoplasm / cytosol
Similarity search - Function
Ribonuclease inhibitor, leucine rich repeat cap / Capping Ribonuclease inhibitor Leucine Rich Repeat / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site ...Ribonuclease inhibitor, leucine rich repeat cap / Capping Ribonuclease inhibitor Leucine Rich Repeat / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Ribonuclease pancreatic / Ribonuclease inhibitor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1999 Å
AuthorsChang, A. / Lomax, J.E. / Bingman, C.A. / Raines, R.T. / Phillips Jr., G.N.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Functional evolution of ribonuclease inhibitor: insights from birds and reptiles.
Authors: Lomax, J.E. / Bianchetti, C.M. / Chang, A. / Phillips, G.N. / Fox, B.G. / Raines, R.T.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
C: Ribonuclease pancreatic
D: Ribonuclease pancreatic
E: Ribonuclease inhibitor
F: Ribonuclease inhibitor
G: Ribonuclease inhibitor
H: Ribonuclease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,55922
Polymers256,6468
Non-polymers91314
Water14,808822
1
A: Ribonuclease pancreatic
E: Ribonuclease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4546
Polymers64,1622
Non-polymers2924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint12 kcal/mol
Surface area22910 Å2
MethodPISA
2
B: Ribonuclease pancreatic
F: Ribonuclease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3485
Polymers64,1622
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint10 kcal/mol
Surface area22540 Å2
MethodPISA
3
C: Ribonuclease pancreatic
G: Ribonuclease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4106
Polymers64,1622
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint2 kcal/mol
Surface area22250 Å2
MethodPISA
4
D: Ribonuclease pancreatic
H: Ribonuclease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3485
Polymers64,1622
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.396, 125.341, 123.064
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer.

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Components

#1: Protein
Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 14171.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6J / Gene: Rib-1, Rib1, Rnase1, Rns1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00683, EC: 3.1.27.5
#2: Protein
Ribonuclease inhibitor / Ribonuclease/angiogenin inhibitor 1


Mass: 49990.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6J / Gene: Rnh, Rnh1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91VI7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: Protein solution mixed in a 1:1 ratio with the well solution (PEG 3350 25%, NaCitrate 100mM pH 3.5), vapor diffusion, hanging drop. cryoprotected with 20% Ethylene Glycol, PEG 3350 25%, and ...Details: Protein solution mixed in a 1:1 ratio with the well solution (PEG 3350 25%, NaCitrate 100mM pH 3.5), vapor diffusion, hanging drop. cryoprotected with 20% Ethylene Glycol, PEG 3350 25%, and NaCitrate 100mM pH 3.5, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2010 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1999→50 Å / Num. obs: 108499 / % possible obs: 97.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.145 / Χ2: 1.086 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1999-2.242.60.47848300.916188.2
2.24-2.282.90.46650350.966190.6
2.28-2.323.20.46350760.961192.5
2.32-2.373.40.42352220.917194.8
2.37-2.423.70.4353360.95196.4
2.42-2.483.90.39553840.951198
2.48-2.544.20.37554860.936199.4
2.54-2.614.40.35655400.962199.9
2.61-2.694.50.3155190.975199.9
2.69-2.774.60.27155311.003199.9
2.77-2.874.70.24154911.0431100
2.87-2.994.70.22255621.0821100
2.99-3.124.70.19455311.1391100
3.12-3.294.70.15555601.1781100
3.29-3.494.70.13454961.2451100
3.49-3.764.70.10355511.3051100
3.76-4.144.70.08455621.291100
4.14-4.744.70.07455671.173199.9
4.74-5.974.70.07555931.1681100
5.97-504.50.07156271.161199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å36.52 Å
Translation2.5 Å36.52 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1999→34.378 Å / Occupancy max: 1 / Occupancy min: 0.89 / FOM work R set: 0.8369 / SU ML: 0.29 / σ(F): 0 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1897 1.86 %
Rwork0.1818 --
obs0.1827 102210 92.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.41 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 100.89 Å2 / Biso mean: 25.5052 Å2 / Biso min: 4.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.6658 Å20 Å20.389 Å2
2--0.5966 Å2-0 Å2
3---0.3418 Å2
Refinement stepCycle: LAST / Resolution: 2.1999→34.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17650 0 59 822 18531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317940
X-RAY DIFFRACTIONf_angle_d0.67924231
X-RAY DIFFRACTIONf_chiral_restr0.0472848
X-RAY DIFFRACTIONf_plane_restr0.0033152
X-RAY DIFFRACTIONf_dihedral_angle_d12.4976833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1999-2.25490.33761110.23365852596376
2.2549-2.31580.24211270.20476274640181
2.3158-2.3840.29661290.19456570669985
2.384-2.46090.30271270.20326810693788
2.4609-2.54880.26591370.20196997713490
2.5488-2.65080.32321330.19827106723992
2.6508-2.77140.25751450.19217338748394
2.7714-2.91750.26321240.18527380750495
2.9175-3.10020.24841380.19337412755096
3.1002-3.33930.23471460.18667574772097
3.3393-3.6750.24441430.16917662780599
3.675-4.2060.1681470.1527735788299
4.206-5.2960.17621380.147978037941100
5.296-34.38180.20031520.19827800795299

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