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Basic information

Entry
Database: PDB / ID: 6ssn
TitleRNASE 3/1 version3
ComponentsRNase 3/1 version3
KeywordsHYDROLASE / RNASE 3/1 version3 / PANCREATIC RIBONUCLEASE
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.511 Å
AuthorsFernandez-Millan, P. / Prats-Ejarque, G. / Vazquez-Monteagudo, S. / Boix, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessSAF2015-66007-P Spain
CitationJournal: Front Mol Biosci / Year: 2022
Title: Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras.
Authors: Fernandez-Millan, P. / Vazquez-Monteagudo, S. / Boix, E. / Prats-Ejarque, G.
History
DepositionSep 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNase 3/1 version3
B: RNase 3/1 version3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,84211
Polymers30,9902
Non-polymers8529
Water5,044280
1
A: RNase 3/1 version3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9676
Polymers15,4951
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNase 3/1 version3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8755
Polymers15,4951
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.381, 39.548, 46.331
Angle α, β, γ (deg.)73.610, 83.110, 66.640
Int Tables number1
Space group name H-MP1

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Components

#1: Protein RNase 3/1 version3


Mass: 15494.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate, pH 6.5 and 1.5 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.51→35.235 Å / Num. obs: 31951 / % possible obs: 84.91 % / Redundancy: 2 % / Biso Wilson estimate: 21.37 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.98
Reflection shellResolution: 1.51→1.56 Å / Mean I/σ(I) obs: 1.59 / Num. unique obs: 3156 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.511→35.235 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.45
RfactorNum. reflection% reflection
Rfree0.2264 1569 4.91 %
Rwork0.1733 --
obs0.1759 31945 84.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.05 Å2 / Biso mean: 25.0611 Å2 / Biso min: 8.96 Å2
Refinement stepCycle: final / Resolution: 1.511→35.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 54 280 2502
Biso mean--35.74 30.9 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.511-1.55970.33391360.2809273084
1.5597-1.61540.31651380.2515269483
1.6154-1.68010.30631540.2471258180
1.6801-1.75660.26911320.2175269583
1.7566-1.84920.25421530.2093267682
1.8492-1.9650.26681530.185276386
1.965-2.11670.24961420.1662260080
2.1167-2.32970.21121380.1565293189
2.3297-2.66670.21511490.1563291390
2.6667-3.35940.18591340.154284287
3.3594-35.2350.19511400.1568295190
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)
16.25462.3444-0.11255.1860.99712.0167-0.0844-0.19430.09890.1917-0.0454-0.07860.07340.10140.07350.09890.02340.00180.13220.01820.12125.51355.4924-14.4603
21.89350.81040.08880.70470.82381.75020.02510.24830.0012-0.504-0.00620.32640.11480.0826-0.1410.34260.05140.03690.24860.03320.178118.0726-6.8441-23.9067
33.96823.3870.86913.26510.68250.3231-0.09090.13190.0933-0.20160.12530.0399-0.10840.1741-0.05490.15270.00110.01970.11890.00040.136828.4933-6.8072-17.8426
41.8292-0.49580.00191.198-0.67030.4519-0.1069-0.1294-0.11-0.02220.08430.0363-0.0154-0.09640.01830.12080.01070.02320.1043-0.00380.147222.8068-4.9946-13.041
54.0459-1.533-1.26112.6940.35154.43860.06320.22830.136-0.26610.01160.0747-0.0078-0.2003-0.13530.1325-0.00910.01670.14690.02150.13419.34277.3495-18.9235
64.0782-1.23872.92562.5299-2.32155.8842-0.0704-0.06260.1850.36760.04950.0299-0.4450.0172-0.10180.182900.02070.11260.00380.12039.53537.5145-3.8566
73.81834.47151.93235.42593.09763.3864-0.1209-0.0130.1991-0.17140.02390.5436-0.1432-0.3678-0.06190.11920.00220.00990.13350.01990.16754.00252.4449-12.3103
87.8274-2.92233.10391.3798-0.83351.8267-0.12450.0453-0.0941-0.1907-0.0183-0.01230.1190.01270.02470.109-0.0240.00850.1248-0.01260.163615.3441-9.1162-14.1207
94.44942.74810.19995.5198-0.29320.14950.2878-0.2006-0.01970.2781-0.1081-0.0663-0.1284-0.0286-0.10360.12620.01650.03180.13850.01630.205932.1116-15.3596-10.7222
103.9584-1.2392-0.88561.19140.02070.3206-0.21430.1555-0.639-0.00540.12450.20780.1611-0.0135-0.08440.1774-0.02320.01760.11240.00950.186113.5718-12.588-14.4661
111.3878-0.75430.18890.5013-0.36671.23190.0648-0.0226-0.10860.1039-0.0434-0.0616-0.1049-0.0543-0.06590.08130.0150.02540.1023-0.01010.140111.59236.3903-10.8099
121.46-0.777-1.13372.344-1.6793.704-0.04-0.1452-0.07750.04880.1892-0.0987-0.1649-0.0789-0.23260.1290.00360.03160.12960.00860.145719.624516.5855-20.5131
131.10610.3806-0.17662.3966-0.58161.2122-0.0507-0.0811-0.1836-0.03420.02670.05010.37-0.038-0.05590.16580.00640.02970.15770.00690.159214.03944.2973-10.4115
143.88591.00421.83582.55341.39073.43020.1896-0.09210.1449-0.0073-0.09060.0676-0.16130.1035-0.00130.1432-0.03010.01110.1241-0.0010.099616.1625-7.186814.9287
152.20730.79161.56210.28780.55891.0934-0.0415-0.24320.1750.16770.29480.5123-0.0322-0.4652-0.06710.20610.05040.07060.25620.06560.2915-0.6425-8.41499.8832
164.77021.56312.29262.56330.98171.92440.2336-0.1359-0.00550.0044-0.1080.0284-0.192-0.2126-0.15740.21790.04460.00720.13890.00320.13645.43680.109113.9584
170.10290.05620.11590.34760.5560.5855-0.0413-0.0498-0.0063-0.13460.02510.0897-0.072-0.07740.03450.18040.02220.01770.13350.00730.132910.4101-8.50778.4219
182.56032.3604-0.70646.1096-1.03492.330.2109-0.10170.1545-0.0969-0.2585-0.08980.10510.2670.0030.20850.02180.0260.16360.01910.127122.3282-15.3763-1.13
197.38261.21762.69940.32160.5561.4970.07920.5212-0.0496-0.2208-0.07740.22190.26270.2137-0.02650.2699-0.00970.00710.1399-0.03280.137612.3208-20.2688-2.0953
200.19340.0241-0.03321.97780.73130.2544-0.0397-0.00190.02120.05650.13690.1994-0.049-0.1394-0.0880.21640.0217-0.02970.15950.01360.16054.1835-6.47581.8176
212.12111.02053.27110.60821.83335.52710.16430.16980.5552-0.30690.0356-0.1335-0.11140.0965-0.09750.26930.05880.04870.1750.0260.23134.616710.20428.6983
221.38820.69510.50710.388-0.00621.1872-0.09810.0772-0.0262-0.2274-0.04520.3339-0.1073-0.3141-0.03480.18960.0376-0.0230.1720.01630.13941.3081-5.1924-0.3388
230.9076-0.3091.10930.3187-0.66662.870.0003-0.0292-0.04380.0066-0.0947-0.03620.11720.08370.08650.1775-0.0020.02970.1202-0.00410.135718.5318-18.377913.136
241.1169-0.40230.33383.5065-2.94244.28590.06770.08960.1657-0.08420.03820.0168-0.1895-0.0006-0.08970.19950.02040.03290.14680.01880.144416.2837-13.20724.4316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 15 )A0 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 22 )A16 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 33 )A23 - 33
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 47 )A34 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 56 )A48 - 56
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 68 )A57 - 68
7X-RAY DIFFRACTION7chain 'A' and (resid 69 through 75 )A69 - 75
8X-RAY DIFFRACTION8chain 'A' and (resid 76 through 83 )A76 - 83
9X-RAY DIFFRACTION9chain 'A' and (resid 84 through 93 )A84 - 93
10X-RAY DIFFRACTION10chain 'A' and (resid 94 through 101 )A94 - 101
11X-RAY DIFFRACTION11chain 'A' and (resid 102 through 109 )A102 - 109
12X-RAY DIFFRACTION12chain 'A' and (resid 110 through 119 )A110 - 119
13X-RAY DIFFRACTION13chain 'A' and (resid 120 through 129 )A120 - 129
14X-RAY DIFFRACTION14chain 'B' and (resid 0 through 15 )B0 - 15
15X-RAY DIFFRACTION15chain 'B' and (resid 16 through 22 )B16 - 22
16X-RAY DIFFRACTION16chain 'B' and (resid 23 through 33 )B23 - 33
17X-RAY DIFFRACTION17chain 'B' and (resid 34 through 56 )B34 - 56
18X-RAY DIFFRACTION18chain 'B' and (resid 57 through 68 )B57 - 68
19X-RAY DIFFRACTION19chain 'B' and (resid 69 through 75 )B69 - 75
20X-RAY DIFFRACTION20chain 'B' and (resid 76 through 83 )B76 - 83
21X-RAY DIFFRACTION21chain 'B' and (resid 84 through 93 )B84 - 93
22X-RAY DIFFRACTION22chain 'B' and (resid 94 through 101 )B94 - 101
23X-RAY DIFFRACTION23chain 'B' and (resid 102 through 119 )B102 - 119
24X-RAY DIFFRACTION24chain 'B' and (resid 120 through 129 )B120 - 129

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