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- PDB-4per: Structure of Gallus gallus ribonuclease inhibitor complexed with ... -

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Basic information

Entry
Database: PDB / ID: 4per
TitleStructure of Gallus gallus ribonuclease inhibitor complexed with Gallus gallus ribonuclease I
Components
  • Angiogenin
  • Ribonuclease Inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / leucine-rich repeat / protein-protein complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Adherens junctions interactions / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / Antimicrobial peptides / Neutrophil degranulation / cytoplasmic vesicle / angiogenesis / endonuclease activity / nucleic acid binding / cell differentiation ...Adherens junctions interactions / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / Antimicrobial peptides / Neutrophil degranulation / cytoplasmic vesicle / angiogenesis / endonuclease activity / nucleic acid binding / cell differentiation / negative regulation of translation / nucleolus / protein homodimerization activity / extracellular region / nucleus / cytoplasm
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 / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Angiogenin / Ribonuclease inhibitor
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 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_assembly_prop / 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_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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 Inhibitor
B: Angiogenin


Theoretical massNumber of molelcules
Total (without water)63,2882
Polymers63,2882
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-6 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.662, 84.538, 121.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease Inhibitor


Mass: 50388.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: RNH1, RCJMB04_22k18 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZIY8
#2: Protein Angiogenin / Ribonuclease A / Ribonuclease I


Mass: 12898.765 Da / Num. of mol.: 1 / Fragment: UNP residues 25-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ANG, RNaseA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P27043, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 1:1 protein solution (20 mM HEPES-NaOH, 10 mM DTT, 2% w/v glycerol, pH 7.5) to well solution (100 mM citric acid, pH 3.5, 21% PEG1500), cryoprotectant: 100 mM citric acid, pH 3.5, 21% ...Details: 1:1 protein solution (20 mM HEPES-NaOH, 10 mM DTT, 2% w/v glycerol, pH 7.5) to well solution (100 mM citric acid, pH 3.5, 21% PEG1500), cryoprotectant: 100 mM citric acid, pH 3.5, 21% 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: Jul 11, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Number: 201341 / Rmerge(I) obs: 0.134 / Χ2: 0.93 / D res high: 1.82 Å / D res low: 50 Å / Num. obs: 50875 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.945010.0320.4933.9
3.924.9410.040.9454.1
3.433.9210.0551.0224.1
3.113.4310.0651.2274.1
2.893.1110.0671.0144.1
2.722.8910.0671.0824.1
2.582.7210.0760.9674
2.472.5810.0831.0274
2.372.4710.0961.0514
2.292.3710.111.0644
2.222.2910.1281.0424
2.162.2210.1451.0264
2.12.1610.1720.9914
2.052.110.2060.9454
22.0510.2470.9023.9
1.96210.3170.8283.9
1.921.9610.3860.8033.8
1.891.9210.4880.763.8
1.851.8910.5650.7093.8
1.821.8510.6870.6913.7
ReflectionResolution: 1.82→50 Å / Num. obs: 50875 / % possible obs: 99.4 % / Redundancy: 4 % / Biso Wilson estimate: 2.21 Å2 / Rmerge(I) obs: 0.134 / Χ2: 0.934 / Net I/av σ(I): 9.161 / Net I/σ(I): 10.4 / Num. measured all: 201341
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.82-1.853.70.68725470.69199.8
1.85-1.893.80.56524630.70999.7
1.89-1.923.80.48825510.76100
1.92-1.963.80.38624820.803100
1.96-23.90.31725240.828100
2-2.053.90.24725210.90299.9
2.05-2.140.20625200.94599.8
2.1-2.1640.17225590.991100
2.16-2.2240.14525181.02699.9
2.22-2.2940.12825201.042100
2.29-2.3740.1125481.06499.9
2.37-2.4740.09625471.05199.9
2.47-2.5840.08325321.02799.8
2.58-2.7240.07625490.96799.6
2.72-2.894.10.06725481.08299.8
2.89-3.114.10.06725741.01499.8
3.11-3.434.10.06525651.22799.4
3.43-3.924.10.05525841.02299.4
3.92-4.944.10.0426160.94598.7
4.94-503.90.03226070.49394

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.45 Å39.81 Å
Translation6.45 Å39.81 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→39.815 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 2064 5.01 %
Rwork0.2023 39152 -
obs0.2049 41216 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.95 Å2 / Biso mean: 30.7346 Å2 / Biso min: 1.49 Å2
Refinement stepCycle: final / Resolution: 1.92→39.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 0 233 4591
Biso mean---33.98 -
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094478
X-RAY DIFFRACTIONf_angle_d1.1586083
X-RAY DIFFRACTIONf_chiral_restr0.052726
X-RAY DIFFRACTIONf_plane_restr0.005785
X-RAY DIFFRACTIONf_dihedral_angle_d14.0291684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.96470.26291260.23372433255992
1.9647-2.01380.23921290.20792496262595
2.0138-2.06820.23341330.19892540267396
2.0682-2.12910.26191330.1982545267896
2.1291-2.19780.29381370.20012575271298
2.1978-2.27640.23961390.20472603274298
2.2764-2.36750.26591360.20212619275598
2.3675-2.47520.2611380.20182601273998
2.4752-2.60570.26031420.21112643278599
2.6057-2.76890.2461400.20022673281399
2.7689-2.98260.25051380.21252631276999
2.9826-3.28270.28391430.21682689283299
3.2827-3.75740.2541410.19122681282299
3.7574-4.73270.22761440.16932708285299
4.7327-39.82330.24441450.21732715286095
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75590.21440.16141.0833-0.01230.50050.0556-0.0942-0.45430.01760.00790.00210.4671-0.0047-0.11280.38430.0010.05630.09270.02980.34990.063431.050161.7756
20.6409-0.14410.27480.8126-0.17390.7533-0.0576-0.0959-0.0681-0.0280.00130.0205-0.0461-0.0527-0.0150.01370.0052-0.00860.02010.0490.0824-2.936959.628465.4875
30.348-0.12160.14250.4218-0.08740.2094-0.0407-0.2513-0.10010.2452-0.0093-0.1043-0.0412-0.1442-0.06280.3481-0.0582-0.14590.41350.12210.18677.531154.656394.1957
42.9835-0.90570.87311.10410.30951.11970.12510.056-0.03590.0466-0.092-0.31550.23960.3411-0.03230.22360.0778-0.00270.34550.20120.412620.380739.829877.8035
55.3906-0.00213.030.57161.00153.4621-0.19960.32290.42210.0055-0.0798-0.3657-0.20420.73180.2820.4813-0.1801-0.25080.71870.32090.964336.763846.371985.5656
64.6907-1.23560.44681.6366-0.68811.26960.0120.21630.2112-0.1538-0.1883-0.30410.02360.29320.17040.19780.0417-0.00510.2980.18350.323113.556548.309174.0814
72.7141-1.04070.35330.64980.38181.1126-0.05510.26350.2173-0.0146-0.1481-0.1934-0.15620.25120.20880.3647-0.1205-0.16160.70570.43990.856730.143446.475786.094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 150 )A0 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 291 )A151 - 291
3X-RAY DIFFRACTION3chain 'A' and (resid 292 through 456 )A292 - 456
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 57 )B3 - 57
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 75 )B58 - 75
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 97 )B76 - 97
7X-RAY DIFFRACTION7chain 'B' and (resid 98 through 115 )B98 - 115

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