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- PDB-2bex: Crystal structure of Placental Ribonuclease Inhibitor in complex ... -

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Basic information

Entry
Database: PDB / ID: 2bex
TitleCrystal structure of Placental Ribonuclease Inhibitor in complex with Human Eosinophil Derived Neurotoxin at 2A resolution
Components
  • NONSECRETORY RIBONUCLEASE
  • RIBONUCLEASE INHIBITOR
KeywordsHYDROLASE/INHIBITOR / COMPLEX (INHIBITOR-NUCLEASE) / RIBONUCLEASE INHIBITOR / EOSINOPHIL DERIVED NEUROTOXIN / RNASE 2 / LUECINE-RICH REPEATS / PROTEIN-PROTEIN INTERACTION / MOLECULAR RECOGNITION / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


ribonuclease inhibitor activity / angiogenin-PRI complex / regulation of Arp2/3 complex-mediated actin nucleation / RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / mRNA catabolic process / RNA nuclease activity / regulation of angiogenesis / innate immune response in mucosa ...ribonuclease inhibitor activity / angiogenin-PRI complex / regulation of Arp2/3 complex-mediated actin nucleation / RNA catabolic process / pancreatic ribonuclease / ribonuclease A activity / mRNA catabolic process / RNA nuclease activity / regulation of angiogenesis / innate immune response in mucosa / chemotaxis / azurophil granule lumen / cell migration / lamellipodium / defense response to virus / nucleic acid binding / lyase activity / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / nucleoplasm / plasma membrane / 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, 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 / 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
ALPHA-KETOMALONIC ACID / Non-secretory ribonuclease / Ribonuclease inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsIyer, S. / Holloway, D.E. / Kumar, K. / Shapiro, R. / Acharya, K.R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Molecular Recognition of Human Eosinophil-Derived Neurotoxin (Rnase 2) by Placental Ribonuclease Inhibitor
Authors: Iyer, S. / Holloway, D.E. / Kumar, K. / Shapiro, R. / Acharya, K.R.
History
DepositionDec 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE INHIBITOR
B: RIBONUCLEASE INHIBITOR
C: NONSECRETORY RIBONUCLEASE
D: NONSECRETORY RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2086
Polymers130,9984
Non-polymers2102
Water11,097616
1
A: RIBONUCLEASE INHIBITOR
C: NONSECRETORY RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5913
Polymers65,4992
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBONUCLEASE INHIBITOR
D: NONSECRETORY RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6173
Polymers65,4992
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.980, 91.980, 257.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 49887.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: PLACENTA / References: UniProt: P13489
#2: Protein NONSECRETORY RIBONUCLEASE / EOSINOPHIL DERIVED NEUROTOXIN / RIBONUCLEASE US / RNASE UPI-2 / RIBONUCLEASE 2 / RNASE 2


Mass: 15611.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: EOSINOPHILS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P10153, EC: 3.1.27.5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MAK / ALPHA-KETOMALONIC ACID


Mass: 118.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growpH: 7 / Details: 1M SODIUM MALONATE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 8, 2002 / Details: MIRROR
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.99→40 Å / Num. obs: 89545 / % possible obs: 99.4 % / Redundancy: 27.6 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4Y, PDB ENTRY 1GQV

1a4y

1gqv


Resolution: 1.99→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1 TO 4 IN CHAIN A AND RESIDUES 1-3 OF CHAIN B ARE MISSING FROM THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 3349 3.8 %RANDOM
Rwork0.2059 ---
obs0.2059 84451 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0146 Å2 / ksol: 0.35745 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--1.454 Å2-1.761 Å20 Å2
2---1.454 Å20 Å2
3---2.909 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.99→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8875 0 14 616 9505
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004619
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.19367
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.11141
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73195
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.731.5
X-RAY DIFFRACTIONc_mcangle_it1.222
X-RAY DIFFRACTIONc_scbond_it1.282
X-RAY DIFFRACTIONc_scangle_it1.952.5
LS refinement shellResolution: 1.99→2.06 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2555 264 7.9 %
Rwork0.24 7659 -
obs--90.34 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MALONATE.PARAMMALONATE.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP

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