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- PDB-4peq: Structure of bovine ribonuclease inhibitor complexed with bovine ... -

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Basic information

Entry
Database: PDB / ID: 4peq
TitleStructure of bovine ribonuclease inhibitor complexed with bovine ribonuclease I
Components
  • Ribonuclease pancreaticPancreatic ribonuclease family
  • Ribonuclease/angiogenin inhibitor 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / leucine-rich repeat / protein-protein complex / 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 / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region ...ribonuclease inhibitor activity / angiogenin-PRI complex / pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / regulation of angiogenesis / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / nucleoplasm / cytosol
Similarity search - Function
Ribonuclease inhibitor, leucine rich repeat cap / Capping Ribonuclease inhibitor Leucine Rich Repeat / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / P-30 Protein / Ribonuclease A-like domain ...Ribonuclease inhibitor, leucine rich repeat cap / Capping Ribonuclease inhibitor Leucine Rich Repeat / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic / Ribonuclease inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.211 Å
AuthorsBianchetti, C.M. / Lomax, J.E. / Raines, R.T. / Fox, B.G.
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
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Structure summary
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease/angiogenin inhibitor 1
C: Ribonuclease pancreatic
D: Ribonuclease/angiogenin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)125,1954
Polymers125,1954
Non-polymers00
Water10,124562
1
A: Ribonuclease pancreatic
B: Ribonuclease/angiogenin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)62,5972
Polymers62,5972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribonuclease pancreatic
D: Ribonuclease/angiogenin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)62,5972
Polymers62,5972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.792, 123.550, 179.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Fragment: UNP residues 27-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61823, EC: 3.1.27.5
#2: Protein Ribonuclease/angiogenin inhibitor 1


Mass: 48889.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNH1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3SZN8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1:1 protein solution (20 mM HEPES-NaOH, 10 mM DTT, 2% w/v glycerol, pH 7.5) to well solution (100 mM malic acid/MES/Tris, pH 4.0, 25% PEG1500), cryoprotectant: 100 mM malic acid/MES/Tris, pH ...Details: 1:1 protein solution (20 mM HEPES-NaOH, 10 mM DTT, 2% w/v glycerol, pH 7.5) to well solution (100 mM malic acid/MES/Tris, pH 4.0, 25% PEG1500), cryoprotectant: 100 mM malic acid/MES/Tris, pH 4.0, 25% PEG1500, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2013
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Number: 470079 / Rmerge(I) obs: 0.084 / Χ2: 1.01 / D res high: 2.21 Å / D res low: 50 Å / Num. obs: 65409 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
65010.051.177.1
4.76610.0510.8597.4
4.164.7610.0611.2077.5
3.784.1610.0591.0317.5
3.513.7810.060.9557.5
3.33.5110.0711.0417.6
3.143.310.0891.0957.5
33.1410.1091.0747.5
2.88310.1291.0377.5
2.782.8810.151.0087.4
2.72.7810.1840.987.4
2.622.710.2210.9577.4
2.552.6210.2560.9587.3
2.492.5510.2930.9817.3
2.432.4910.3460.9697.3
2.382.4310.4340.9477.2
2.332.3810.5040.9547
2.292.3310.5580.9556.4
2.252.2910.6320.9436
2.212.2510.7470.9425.6
ReflectionResolution: 2.21→50 Å / Num. obs: 65409 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.37 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.006 / Net I/av σ(I): 22.722 / Net I/σ(I): 10.7 / Num. measured all: 470079
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.21-2.255.60.74731800.94299.4
2.25-2.2960.63232500.943100
2.29-2.336.40.55832470.955100
2.33-2.3870.50432320.954100
2.38-2.437.20.43432400.947100
2.43-2.497.30.34632330.969100
2.49-2.557.30.29332370.981100
2.55-2.627.30.25632650.958100
2.62-2.77.40.22132370.957100
2.7-2.787.40.18432280.98100
2.78-2.887.40.1532971.008100
2.88-37.50.12932451.037100
3-3.147.50.10932511.074100
3.14-3.37.50.08932911.095100
3.3-3.517.60.07132681.041100
3.51-3.787.50.0632790.955100
3.78-4.167.50.05932991.031100
4.16-4.767.50.06133281.207100
4.76-67.40.05133250.859100
6-507.10.0534771.1799.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.21 Å49.22 Å
Translation8.38 Å49.22 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.211→49.224 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1930 3.24 %
Rwork0.1756 57584 -
obs0.1773 59514 90.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.8 Å2 / Biso mean: 20.5454 Å2 / Biso min: 4.07 Å2
Refinement stepCycle: final / Resolution: 2.211→49.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8673 0 0 562 9235
Biso mean---23.69 -
Num. residues----1156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088814
X-RAY DIFFRACTIONf_angle_d1.19211938
X-RAY DIFFRACTIONf_chiral_restr0.0721423
X-RAY DIFFRACTIONf_plane_restr0.0051557
X-RAY DIFFRACTIONf_dihedral_angle_d14.0753288
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 (%)
2.211-2.26590.2984680.21751916198443
2.2659-2.32720.2632920.20362973306566
2.3272-2.39560.26211260.19823873399987
2.3956-2.4730.24781510.18344163431493
2.473-2.56130.231400.18584238437895
2.5613-2.66390.25281480.19234287443596
2.6639-2.78510.2371340.19794341447596
2.7851-2.93190.28831530.19454424457798
2.9319-3.11560.23381530.19984446459998
3.1156-3.35610.26261530.19484501465499
3.3561-3.69370.21221580.164144944652100
3.6937-4.2280.19681430.146545724715100
4.228-5.32580.17011470.147546064753100
5.3258-49.23620.23021640.177347504914100

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