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- PDB-2bnh: PORCINE RIBONUCLEASE INHIBITOR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2bnh
TitlePORCINE RIBONUCLEASE INHIBITOR
ComponentsRIBONUCLEASE INHIBITOR
KeywordsACETYLATION / LEUCINE-RICH REPEATS
Function / homology
Function and homology information


ribonuclease inhibitor activity / angiogenin-PRI complex / regulation of Arp2/3 complex-mediated actin nucleation / regulation of angiogenesis / cell migration / lamellipodium / nucleoplasm / nucleus / plasma membrane / 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, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe ...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, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Ribonuclease inhibitor
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKobe, B. / Deisenhofer, J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A.
Authors: Kobe, B. / Deisenhofer, J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of Porcine Ribonuclease Inhibitor, a Protein with Leucine-Rich Repeats
Authors: Kobe, B. / Deisenhofer, J.
#2: Journal: Nature / Year: 1993
Title: Crystal Structure of Porcine Ribonuclease Inhibitor, a Protein with Leucine-Rich Repeats
Authors: Kobe, B. / Deisenhofer, J.
History
DepositionJun 29, 1996Processing site: BNL
SupersessionMar 12, 1997ID: 1BNH
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)49,0921
Polymers49,0921
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.900, 134.900, 83.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein RIBONUCLEASE INHIBITOR / RNASE INHIBITOR / RIBONUCLEASE/ANGIOGENIN INHIBITOR


Mass: 49092.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: LIVER / References: UniProt: P10775
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlRI1drop
28.9 mMpotassium phosphate1drop
317.8 mMdithiothreitol1drop
43.1 mg/mlRNase A1drop
50.58 Mammonium sulfate1drop
644.4 mMsodium acetate1drop
71.3 Mammonium sulfate1reservoir
8100 mMsodium acetate1reservoir
920 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 24468 / % possible obs: 73.2 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→40 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.2 -
obs0.2 24468
Displacement parametersBiso mean: 30.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati sigma a obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 0 64 3478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.676
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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