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- PDB-1z7x: X-ray structure of human ribonuclease inhibitor complexed with ri... -

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Basic information

Entry
Database: PDB / ID: 1z7x
TitleX-ray structure of human ribonuclease inhibitor complexed with ribonuclease I
Components
  • Ribonuclease I
  • Ribonuclease inhibitor
KeywordsHydrolase/Hydrolase INHIBITOR / RIBONUCLEASE-INHIBITOR COMPLEX / LEUCINE-RICH REPEAT / ENZYME-INHIBITOR COMPLEX / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / Center for Eukaryotic Structural Genomics / Hydrolase-Hydrolase INHIBITOR COMPLEX
Function / homology
Function and homology information


ribonuclease inhibitor activity / angiogenin-PRI complex / regulation of Arp2/3 complex-mediated actin nucleation / pancreatic ribonuclease / ribonuclease A activity / mRNA catabolic process / RNA nuclease activity / regulation of angiogenesis / Late endosomal microautophagy / Chaperone Mediated Autophagy ...ribonuclease inhibitor activity / angiogenin-PRI complex / regulation of Arp2/3 complex-mediated actin nucleation / pancreatic ribonuclease / ribonuclease A activity / mRNA catabolic process / RNA nuclease activity / regulation of angiogenesis / Late endosomal microautophagy / Chaperone Mediated Autophagy / cell migration / lamellipodium / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome / 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
CITRIC ACID / Ribonuclease pancreatic / Ribonuclease inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMcCoy, J.G. / Johnson, R.J. / Raines, R.T. / Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Allard, S.T.M. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein.
Authors: Johnson, R.J. / McCoy, J.G. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T.
History
DepositionMar 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET DETERMINATION METHOD:AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Ribonuclease I
W: Ribonuclease inhibitor
Z: Ribonuclease I
Y: Ribonuclease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6865
Polymers129,4944
Non-polymers1921
Water15,385854
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.338, 107.546, 155.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease I / RNase 1 / RNase A / RNase UpI-1 / RIB-1 / HP-RNase


Mass: 14728.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE1, RIB1, RNS1 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07998, EC: 3.1.27.5
#2: Protein Ribonuclease inhibitor / Ribonuclease/angiogenin inhibitor / RAI / RNase inhibitor / RI


Mass: 50018.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNH, PRI / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13489
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / pH: 4.2
Details: 10% MEPEG 2000, 0.020 M SODIUM CITRATE, 0.025 M DTT, 0.001 M AMMONIUM SULFATE, vapor diffusion, HANGING DROP, temperature 293K, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionRedundancy: 6.8 % / Number: 84446 / Rmerge(I) obs: 0.078 / Χ2: 1.019 / D res high: 1.95 Å / D res low: 50 Å / % possible obs: 97
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.815099.710.0340.8627.1
3.824.8110010.0491.0657.4
3.333.8210010.0561.0257.5
3.033.3310010.0631.0527.5
2.813.0310010.0841.0117.5
2.652.8110010.0991.057.5
2.512.6510010.1311.0557.5
2.42.5110010.161.0627.5
2.312.410010.2081.0627.5
2.232.3110010.2470.987.3
2.162.2310010.2841.0476.8
2.12.1699.610.3091.0626.1
2.052.196.610.3670.8515.2
22.0585.810.3991.0164.5
1.95272.610.4241.0373.6
ReflectionResolution: 1.95→47.19 Å / Num. obs: 84446 / % possible obs: 97 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.964
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.939 / % possible all: 72.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.536 / Cor.coef. Fo:Fc: 0.319
Highest resolutionLowest resolution
Rotation3 Å47.17 Å
Translation3 Å47.17 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DFJ

1dfj


Resolution: 1.95→47.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.762 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4225 5 %RANDOM
Rwork0.175 ---
obs0.178 80141 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8930 0 13 854 9797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0219064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9912265
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5851168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13824.924394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.014151648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2111568
X-RAY DIFFRACTIONr_chiral_restr0.1030.21426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026736
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.24284
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.26128
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2770
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.626032
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.69749344
X-RAY DIFFRACTIONr_scbond_it5.20163404
X-RAY DIFFRACTIONr_scangle_it7.23982921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 239 -
Rwork0.222 4385 -
obs--72.84 %

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