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- PDB-6yo1: Crystal structure of ribonuclease A solved by vanadium SAD phasing -

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Basic information

Entry
Database: PDB / ID: 6yo1
TitleCrystal structure of ribonuclease A solved by vanadium SAD phasing
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Endoribonuclease
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
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
URIDINE-2',3'-VANADATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsEl Omari, K. / Mohamad, N. / Bountra, K. / Duman, R. / Romano, M. / Schlegel, K. / Kwong, H. / Mykhaylyk, V. / Olesen, C.E. / Moller, J.V. ...El Omari, K. / Mohamad, N. / Bountra, K. / Duman, R. / Romano, M. / Schlegel, K. / Kwong, H. / Mykhaylyk, V. / Olesen, C.E. / Moller, J.V. / Bublitz, M. / Beis, K. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N020103/1 United Kingdom
CitationJournal: Iucrj / Year: 2020
Title: Experimental phasing with vanadium and application to nucleotide-binding membrane proteins.
Authors: El Omari, K. / Mohamad, N. / Bountra, K. / Duman, R. / Romano, M. / Schlegel, K. / Kwong, H.S. / Mykhaylyk, V. / Olesen, C. / Moller, J.V. / Bublitz, M. / Beis, K. / Wagner, A.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)28,1034
Polymers27,4172
Non-polymers6862
Water1,53185
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0512
Polymers13,7081
Non-polymers3431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0512
Polymers13,7081
Non-polymers3431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.510, 32.660, 72.400
Angle α, β, γ (deg.)90.000, 90.825, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

21B-303-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTHRTHR(chain 'A' and (resid 2 through 17 or resid 22...AA2 - 172 - 17
12SERSERTHRTHR(chain 'A' and (resid 2 through 17 or resid 22...AA22 - 3622 - 36
13ASPASPTYRTYR(chain 'A' and (resid 2 through 17 or resid 22...AA38 - 9738 - 97
14THRTHRVALVAL(chain 'A' and (resid 2 through 17 or resid 22...AA99 - 12499 - 124
15UVCUVCUVCUVC(chain 'A' and (resid 2 through 17 or resid 22...AC201
26GLUGLUTHRTHR(chain 'B' and (resid 2 through 17 or resid 22...BB2 - 172 - 17
27SERSERTHRTHR(chain 'B' and (resid 2 through 17 or resid 22...BB22 - 3622 - 36
28ASPASPTYRTYR(chain 'B' and (resid 2 through 17 or resid 22...BB38 - 9738 - 97
29THRTHRVALVAL(chain 'B' and (resid 2 through 17 or resid 22...BB99 - 12499 - 124
210UVCUVCUVCUVC(chain 'B' and (resid 2 through 17 or resid 22...BD201

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Components

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


Mass: 13708.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-UVC / URIDINE-2',3'-VANADATE


Mass: 343.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O9V / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 mM sodium citrate pH 5.5, 28 % PEG 4000 with 20 mM uridine/ortho-vanadate

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Data collection

DiffractionMean temperature: 60 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.26 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Aug 1, 2019
RadiationMonochromator: Silicon crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.26 Å / Relative weight: 1
ReflectionResolution: 1.9→41.56 Å / Num. obs: 18916 / % possible obs: 100 % / Redundancy: 23.6 % / Biso Wilson estimate: 35.71 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 18.3 % / Num. unique obs: 1194 / CC1/2: 0.57 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→41.56 Å / SU ML: 0.2373 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2674
RfactorNum. reflection% reflection
Rfree0.2129 878 4.64 %
Rwork0.1859 --
obs0.1872 18911 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 42 85 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071968
X-RAY DIFFRACTIONf_angle_d1.19552670
X-RAY DIFFRACTIONf_chiral_restr0.3203296
X-RAY DIFFRACTIONf_plane_restr0.0059343
X-RAY DIFFRACTIONf_dihedral_angle_d15.9973734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.32511510.28132950X-RAY DIFFRACTION99.81
2.02-2.170.30671430.23972973X-RAY DIFFRACTION99.94
2.17-2.390.24851370.22352999X-RAY DIFFRACTION100
2.39-2.740.26431430.21032992X-RAY DIFFRACTION100
2.74-3.450.25161360.19353022X-RAY DIFFRACTION99.97
3.45-41.560.1591680.15243097X-RAY DIFFRACTION100
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)
13.2581908674-0.4417923407-0.3952437788122.15884901712-1.069964716774.121146273120.4768573188640.3347745032070.9707888724220.0305938997615-0.148954918524-0.306646359303-1.048548531750.634459896925-0.1980137702440.472817555316-0.01632263120990.1232377568440.3618782329390.0589487952260.40263620466232.848104985931.655973928610.4544345452
21.59062553364-3.04020178392-2.313605968496.07818268754.663062595333.579586633920.1259350437310.734192500697-0.597323884298-0.71384805347-0.3163684334350.606943362167-0.468069858651-0.8356315162680.05420931413030.627656704560.0518242731842-0.0550342633670.7464460478040.01871327358140.45602633505225.853470553220.1342712588-0.379428403792
33.36507532661-0.947850549043-0.9218114483243.514816941080.5012120870653.250015555680.1516086103150.2608625735980.211760977086-0.640098720385-0.0196563930447-0.838320362526-0.2128235608070.0516442103922-0.1339090439090.43018193751-0.02578234713840.0724227376240.460859508767-0.002125281154670.39984237939635.051564014123.36576914772.66981270839
43.36370648146-1.050568183661.397929002452.56835877868-1.407983160993.20860664842-0.05578644482620.00527298528305-0.01738129171290.04924736995450.09173546920250.025865956305-0.28076115907-0.337941760196-0.01122459977110.2833728521580.01179894456380.005463120794050.3083885816940.005804771198120.27232276536527.292010870522.461037113721.9175761546
55.612098227640.251148007549-0.4479441869311.79784909679-1.617126261711.85860407613-0.4143971964150.35759055230.0960446407764-0.0321608175520.4303211378430.2114679594380.161428099855-0.426949672775-0.01316810110240.355195623456-0.0260538705208-0.01006213629790.360236770985-0.007009555721180.35108517209423.350610690517.583112718520.641091135
66.31144135027-0.223847543067-2.208863962541.87851593979-0.3742682329572.88865155834-0.06822446030730.315291928971-0.0517746291468-0.5206689004050.113426168666-0.6297290391960.7007634352630.271437188258-0.02959082470020.499323466031-0.02407644498660.08607055185120.566744041765-0.06810972494640.51730657078539.332965991617.33325344581.30596218843
72.06529702879-0.576688436447-0.6378362021510.723520084369-0.6713239575812.1993154656-0.12412759830.246857680688-0.0326440463266-0.01768571732530.206727232627-0.1235539902290.378459271849-0.286659186569-0.06257317977680.303025805743-0.01255958063060.01144993540750.316941689976-0.003268419532710.32039699140329.568685377520.683785107514.4280388151
83.587475686631.5841614550.2305016243552.69707005356-0.1571527413593.33688934602-0.246570123876-0.165874287195-0.413501595786-0.0006813247875580.3920000761040.1666494439390.180049590464-0.0741995791477-0.08244509861790.3276469181990.03059953980260.02598391494240.3503562840240.01246492739530.39534890340133.1233476566-1.691397398741.8957240972
94.07322146-0.313885820370.8645975640641.78116772648-1.021636125763.14607899491-0.368955732716-0.6880338290770.1153687789410.7972420043120.265357826931-0.0817246246877-0.485163060381-0.2407118759370.09526871611840.3804757150480.0831176703678-0.02518478138790.441172351062-0.06245544804930.32710820906939.75761653496.2592310979549.4649539682
103.45296256776-0.89539349143-1.657840676972.693428754590.7066049756652.90003002106-0.1106187709210.369374313315-0.121118501947-0.150896778869-0.0326914897465-0.104267565182-0.00660128317506-0.05167781021340.1540815344140.252436064724-0.02486331409760.0005292294137940.273125302047-0.001677977522460.33182720464937.52277755284.7851261475828.713750131
111.93282369115-0.1818141234640.9355147535571.63926982163-0.06940795872612.2977794763-0.0697028206527-0.155925910615-0.04417000153620.3002335491840.0184612176275-0.304602927701-0.08484762019340.1633245991830.05384547115810.3031852535480.00191278806054-0.04156797413040.29512354682-0.01460661649480.36184431410442.56685851126.1158914067340.09382745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 50 )
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 96 )
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 124 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 12 )
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 50 )
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 124 )

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