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- PDB-3mwq: Crystal structure of ribonuclease A tandem enzymes and their inte... -

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Basic information

Entry
Database: PDB / ID: 3mwq
TitleCrystal structure of ribonuclease A tandem enzymes and their interaction with the cytosolic ribonuclease inhibitor
ComponentsRibonuclease pancreatic, LINKER, Ribonuclease pancreatic
KeywordsHYDROLASE / ribonuclease A tandem enzyme / SGRSGRSG-linker
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsNeumann, P. / Leich, F.
CitationJournal: Febs J. / Year: 2011
Title: Crystal structure of RNase A tandem enzymes and their interaction with the cytosolic ribonuclease inhibitor
Authors: Arnold, U. / Leich, F. / Neumann, P. / Lilie, H. / Ulbrich-Hofmann, R.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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, LINKER, Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8108
Polymers28,1451
Non-polymers6657
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.632, 32.915, 73.391
Angle α, β, γ (deg.)90.000, 91.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28145.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNS1 / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 30% PEG 8000, 0.2M ammonium sulfate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→73.379 Å / Num. all: 29704 / Num. obs: 27506 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 23.786 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 5.949
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.743.20.2822.7777224610.28257.4
1.74-1.8440.1973.81486237300.19791.5
1.84-1.974.40.1335.51674238190.133100
1.97-2.134.40.0927.41580335590.092100
2.13-2.334.50.0689.41482133000.068100
2.33-2.614.50.05411.21344429740.054100
2.61-3.014.60.04612.71209926540.046100
3.01-3.694.60.04510.71028222490.045100
3.69-5.224.50.0499.6796117530.049100
5.22-24.464.40.0499.6439210070.04999.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.499 / Cor.coef. Fo:Fc: 0.345 / Cor.coef. Io to Ic: 0.332
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SRN

1srn


Resolution: 1.68→24.46 Å / Occupancy max: 1 / Occupancy min: 0.11 / SU ML: 0.2 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.42 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1352 5.05 %RANDOM
Rwork0.174 ---
obs0.176 26794 95.16 %-
all-29704 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.417 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 92.07 Å2 / Biso mean: 31.839 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.789 Å2-0 Å2-0.403 Å2
2---4.426 Å2-0 Å2
3---3.638 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.189 Å0.1334 Å
Luzzati d res low-6 Å
Luzzati sigma a0.193 Å0.165 Å
Refinement stepCycle: LAST / Resolution: 1.68→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 37 274 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042076
X-RAY DIFFRACTIONf_angle_d0.9092799
X-RAY DIFFRACTIONf_chiral_restr0.064301
X-RAY DIFFRACTIONf_plane_restr0.004368
X-RAY DIFFRACTIONf_dihedral_angle_d14.053752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.68-1.740.262740.2081705177964
1.74-1.810.2651040.1882332243688
1.81-1.8920.1931240.18326562780100
1.892-1.9920.2351520.16826362788100
1.992-2.1160.2261370.16626692806100
2.116-2.280.1871590.17226482807100
2.28-2.5090.2211380.17126672805100
2.509-2.8720.2031420.17726742816100
2.872-3.6160.2161710.15926812852100
3.616-24.4620.2121510.17527742925100
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)
13.2458-0.4462-2.41822.2956-2.87274.01470.58250.65830.4781-0.2422-0.2843-0.1078-0.4877-0.2976-0.27390.32530.07250.09590.27880.09740.192332.2058.980610.7038
21.6140.19660.52924.39551.8334-2.22880.0070.80390.01-0.45170.3910.0801-0.25830.2029-0.3980.58560.23330.05810.99160.04730.452426.3033-2.9486-2.171
37.16551.4959-3.42863.7487-1.42521.02140.23520.943-0.016-0.99520.1629-0.3998-0.408-0.5933-0.22330.36160.0890.16230.45370.07970.19738.81352.94311.4823
42.1897-0.3415-1.24850.7238-0.71111.3212-0.05260.3674-0.095-0.0351-0.0254-0.052-0.0212-0.32890.06790.1461-0.01060.00070.1737-0.01180.117628.2342-1.1316.3162
50.7158-0.48060.79560.33750.2735-1.75690.15481.09430.0552-0.5744-0.2448-0.1718-0.0443-0.56350.11110.46620.0170.19280.6279-0.07250.365745.424-2.7221-2.6553
62.8963-0.39271.26223.29290.33480.6197-0.1225-0.2139-0.8982-0.65660.3085-0.29940.12220.0157-0.14640.47480.02140.03570.2949-0.08260.573825.6577-14.782421.409
72.07950.41030.40280.7971-0.8047-0.5647-0.15570.76940.0124-0.26530.1083-0.0810.09290.19720.00910.1492-0.0133-0.00950.2499-0.00280.093115.265-3.993430.2914
80.2626-0.23020.59690.76560.1047-0.77260.22490.12720.2644-0.06590.21480.37160.0094-0.0954-0.28350.4422-0.1764-0.16980.69060.34650.580810.393210.069122.9242
93.17340.06792.0563.40080.0386-2.2019-0.04551.26870.0915-0.74360.00970.0435-0.01290.41970.01890.21580.0040.01440.4348-0.02870.09197.3163-4.463119.8039
101.77050.29190.29150.2430.56130.7869-0.11850.07690.0565-0.0097-0.00970.0709-0.06020.03660.10990.1281-0.0091-0.01010.12860.01440.16919.01441.110136.9812
113.2626-0.25021.7702-0.451-0.09181.82440.16660.4293-0.3466-0.0713-0.13220.0615-0.18330.1232-0.01930.38250.0169-0.05240.6217-0.17360.3391-1.2096-8.229414.85
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1(SEGID A AND RESID 1:15)1 - 15
2X-RAY DIFFRACTION2(SEGID A AND RESID 16:24)16 - 24
3X-RAY DIFFRACTION3(SEGID A AND RESID 25:42)25 - 42
4X-RAY DIFFRACTION4(SEGID A AND (RESID 43:86 OR RESID 98:124))0
5X-RAY DIFFRACTION5(SEGID A AND RESID 87:97)87 - 97
6X-RAY DIFFRACTION6(SEGID A AND RESID 125:134)125 - 134
7X-RAY DIFFRACTION7(SEGID A AND RESID 135:146)135 - 146
8X-RAY DIFFRACTION8(SEGID A AND RESID 147:155)147 - 155
9X-RAY DIFFRACTION9(SEGID A AND RESID 156:172)156 - 172
10X-RAY DIFFRACTION10(SEGID A AND (RESID 173:220 OR RESID 228:256))0
11X-RAY DIFFRACTION11(SEGID A AND RESID 221:227)221 - 227

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