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- PDB-3mx8: Crystal structure of ribonuclease A tandem enzymes and their inte... -

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Basic information

Entry
Database: PDB / ID: 3mx8
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 / GPPG-linker
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.1 Å
AuthorsLeich, F. / Neumann, P. / Lilie, H. / Ulbrich-Hofmann, R. / Arnold, U.
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 7, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 1.4Nov 13, 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)28,2237
Polymers27,7071
Non-polymers5166
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.607, 32.667, 73.188
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

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


Mass: 27707.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.17 Å3/Da / Density % sol: 43.3 % / Mosaicity: 0.813 °
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 9, 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: 2.1→73.151 Å / Num. all: 14153 / Num. obs: 14239 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 32.261 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 5.397
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.3 / Num. measured all: 8347 / Num. unique all: 2056 / Rsym value: 0.577 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3MWQ

3mwq


Resolution: 2.1→29.142 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.34 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.43 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 714 5.02 %RANDOM
Rwork0.179 ---
obs0.183 14234 99.92 %-
all-14253 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.188 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 114.75 Å2 / Biso mean: 40.734 Å2 / Biso min: 17.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.194 Å2-0 Å22.371 Å2
2--0.923 Å2-0 Å2
3---0.272 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.334 Å0.301 Å
Luzzati d res low-7 Å
Luzzati sigma a0.354 Å0.321 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 26 211 2160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062003
X-RAY DIFFRACTIONf_angle_d0.992703
X-RAY DIFFRACTIONf_chiral_restr0.062294
X-RAY DIFFRACTIONf_plane_restr0.006355
X-RAY DIFFRACTIONf_dihedral_angle_d15.404722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.2620.3411380.2526592797
2.262-2.490.2381480.19826872835
2.49-2.850.3011310.18126802811
2.85-3.5890.2541560.1626972853
3.589-29.1450.2221410.16327972938
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)
12.77480.2956-1.08220.4497-0.09010.88990.13680.3488-0.1578-0.2879-0.0028-0.02870.0308-0.2362-0.09730.25890.03950.03060.31910.10420.104731.67069.105110.8897
2-0.9471-1.25052.20982.00863.12823.9213-0.79840.561-0.1134-0.12250.59121.18030.03370.77050.4240.60620.04880.18931.3240.11220.696526.0167-2.2469-2.359
37.07331.713-4.22533.70390.23143.43140.4640.7546-0.1412-0.7172-0.1114-0.4866-0.5659-0.6136-0.33690.34720.07280.09530.5496-0.00310.221738.48013.29841.6101
42.2013-0.3546-1.18881.58820.0683-0.3476-0.07080.5824-0.0863-0.02420.02310.07560.0431-0.28220.05940.1892-0.0195-0.01110.2956-0.02660.128427.7156-1.031816.2555
53.68471.3127-0.04488.6783-1.1894.37170.45740.29850.2661-0.6852-1.1496-0.4154-0.0563-0.47220.77850.33990.0350.15890.5926-0.03440.377545.0021-2.3712-2.6761
6-1.09493.3035-1.97972.5455-1.1501-0.48070.1070.60490.02580.3655-0.1880.223-0.0364-0.04760.28130.18270.0942-0.05880.3292-0.07360.212519.6344-11.993127.451
70.69011.10090.15852.4317-1.63832.24460.02330.32740.12840.1162-0.0972-0.14820.15230.2331-0.00490.1947-0.0676-0.02980.32070.01510.172113.79380.1928.3658
82.3421.4998-5.19354.9349-1.7816-5.511-0.31550.87510.3732-0.4604-0.5934-0.0452-0.29490.65520.67490.4475-0.1342-0.24560.55040.18470.26744.83046.541919.6141
92.3798-0.92442.29435.20342.39922.42030.22510.9261-0.1605-0.4578-0.11250.26460.09080.9632-0.08620.21380.0552-0.00670.3691-0.01030.19716.4837-5.866721.1888
101.6739-0.25060.8673-0.03850.35591.8446-0.0183-0.077-0.0461-0.0905-0.00160.1227-0.08310.0260.01320.1438-0.011-0.02250.1117-0.00580.20348.32840.308936.9184
113.0591-1.07672.41483.5187-2.92220.59960.30220.7991-0.1951-1.1158-0.38080.15660.1598-0.28960.09490.37470.0431-0.13640.53510.01250.2415-0.4575-2.395218.0281
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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