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- PDB-1z6d: Ribonuclease A- IMP complex -

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Basic information

Entry
Database: PDB / ID: 1z6d
TitleRibonuclease A- IMP complex
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RIBONUCLEASE
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.54 Å
AuthorsHatzopoulos, G.N. / Leonidas, D.D. / Kardakaris, R. / Kobe, J. / Oikonomakos, N.G.
CitationJournal: Febs J. / Year: 2005
Title: The binding of IMP to Ribonuclease A
Authors: Hatzopoulos, G.N. / Leonidas, D.D. / Kardakaris, R. / Kobe, J. / Oikonomakos, N.G.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1587
Polymers27,4172
Non-polymers1,7415
Water6,485360
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7534
Polymers13,7081
Non-polymers1,0453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4053
Polymers13,7081
Non-polymers6962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Ribonuclease pancreatic
hetero molecules

B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8096
Polymers27,4172
Non-polymers1,3934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4110 Å2
ΔGint-18 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.032, 32.692, 72.474
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2082-

HOH

21B-2091-

HOH

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Components

#1: Protein Ribonuclease pancreatic / Ribonuclease A / RNase A / RNase 1


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.2 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20mM sodium citrate, 20% PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8115 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2004
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8115 Å / Relative weight: 1
ReflectionResolution: 1.54→60 Å / Num. all: 32622 / Num. obs: 32622 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.375 Å2 / Rsym value: 0.041 / Net I/σ(I): 18.7
Reflection shellResolution: 1.54→1.58 Å / Mean I/σ(I) obs: 7.6 / Rsym value: 0.199 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1afu

1afu


Resolution: 1.54→19.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.518 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23433 1675 4.9 %RANDOM
Rwork0.18704 ---
all0.18938 32622 --
obs0.18938 32622 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.29 Å2
2--0.44 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.54→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 115 360 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212067
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9972818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92725.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61815336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.543158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021521
X-RAY DIFFRACTIONr_nbd_refined0.2120.21004
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.269
X-RAY DIFFRACTIONr_mcbond_it0.971.51265
X-RAY DIFFRACTIONr_mcangle_it1.65122008
X-RAY DIFFRACTIONr_scbond_it2.2513925
X-RAY DIFFRACTIONr_scangle_it3.6174.5810
LS refinement shellResolution: 1.538→1.578 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 78 -
Rwork0.205 2145 -
obs-2145 100 %

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