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- PDB-7q76: Room temperature structure of RNase A at 22 MPa helium gas pressu... -

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Basic information

Entry
Database: PDB / ID: 7q76
TitleRoom temperature structure of RNase A at 22 MPa helium gas pressure in a sapphire capillary
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLieske, J. / Guenther, S. / Saouane, S. / Meents, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0405A Germany
CitationJournal: To Be Published
Title: Fixed-target high-pressure macromolecular crystallography
Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / Gabdulkhakov, A.G. / Selikhanov, G.K. / Chapman, H.N. / Meents, A.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: 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: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0307
Polymers13,7081
Non-polymers3216
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-60 kcal/mol
Surface area7000 Å2
Unit cell
Length a, b, c (Å)64.420, 64.420, 65.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Production host: Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10-20 mg/ml protein dissolved in 0.1 M sodium acetate pH 4.5 was mixed in a 1:1 ratio with precipitant containing 0.1 M sodium acetate pH 4.5, 1.2-1.5 M ammonium sulphate and 2-2.5 M sodium ...Details: 10-20 mg/ml protein dissolved in 0.1 M sodium acetate pH 4.5 was mixed in a 1:1 ratio with precipitant containing 0.1 M sodium acetate pH 4.5, 1.2-1.5 M ammonium sulphate and 2-2.5 M sodium chloride and equilibrated for one to two days at room-temperature.
Pressure: 101.325 kPa

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Data collection

DiffractionAmbient environment: gaseous He / Ambient pressure: 22000 kPa / Mean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.477 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Sep 26, 2019
Diffraction measurementSpecimen support: sapphire capillary
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.477 Å / Relative weight: 1
ReflectionResolution: 1.48→25.65 Å / Num. obs: 26313 / % possible obs: 99.17 % / Redundancy: 8.4 % / Biso Wilson estimate: 21.28 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.0485 / Net I/σ(I): 7.44
Reflection shellResolution: 1.48→1.533 Å / Rmerge(I) obs: 2.128 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 2593 / CC1/2: 0.304 / CC star: 0.683 / Rpim(I) all: 0.7747 / % possible all: 98.67
Cell measurementPressure: 22000 kPa

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.13-2998_9999refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E3W

2e3w


Resolution: 1.48→25.65 Å / SU ML: 0.1793 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0956 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.18 2075 7.89 %
Rwork0.1493 24228 -
obs0.1516 26303 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.17 Å2
Refinement stepCycle: LAST / Resolution: 1.48→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 14 77 1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141085
X-RAY DIFFRACTIONf_angle_d1.29051491
X-RAY DIFFRACTIONf_chiral_restr0.0897164
X-RAY DIFFRACTIONf_plane_restr0.0089196
X-RAY DIFFRACTIONf_dihedral_angle_d15.1459441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.30071400.29691548X-RAY DIFFRACTION98.25
1.51-1.550.3361360.27151612X-RAY DIFFRACTION98.92
1.55-1.590.30291390.25351583X-RAY DIFFRACTION98.85
1.59-1.640.23961390.22891584X-RAY DIFFRACTION98.91
1.64-1.690.2291380.20681599X-RAY DIFFRACTION99.31
1.69-1.750.22561340.17841586X-RAY DIFFRACTION99.14
1.75-1.820.20411360.16451606X-RAY DIFFRACTION99.09
1.82-1.910.17811360.14831615X-RAY DIFFRACTION99.6
1.91-2.010.17111370.13271598X-RAY DIFFRACTION99.43
2.01-2.130.16381320.12471628X-RAY DIFFRACTION99.55
2.13-2.30.15231380.13241623X-RAY DIFFRACTION99.55
2.3-2.530.18261350.13981642X-RAY DIFFRACTION99.66
2.53-2.90.18631420.15081625X-RAY DIFFRACTION99.55
2.9-3.650.16311470.14251659X-RAY DIFFRACTION99.29
3.65-25.650.15861460.13241720X-RAY DIFFRACTION99.15
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)
10.216146220704-0.224739301821-0.1309268391560.512662284024-0.125222148430.6343647425620.02018433255770.03819348314960.143546957153-0.07085769255370.07118792070970.342712402626-0.0880707147498-0.358045515663-2.58905415456E-50.183213786608-0.0254788667195-0.005072253820820.1814931062780.001319487765410.20634459138919.4942613076-15.78319075382.77685488151
20.9288492292631.106475349390.006152465699743.87187732112-0.1725416973462.74109335407-0.1474047911270.2614721130480.0685542604757-0.5115357374460.09993258211350.130126744970.0231592436996-0.01155067349565.37659312949E-50.23087642964-0.047241054702-0.01937008623480.194229950765-0.008536916690620.16628374865527.3203308452-8.02825913992-3.7504288646
31.042803540161.108936219050.2810058819151.280241289920.1396054085081.25942034717-0.0423154083821-0.1444559073410.1314937057350.143640703474-0.106701799310.1277522570280.0593026146063-0.364060861839-0.001181657638910.2167767283330.0350869120951-0.0187974530050.229834730683-0.01948141725570.20555485744824.8545549942-11.935075508117.2021745753
40.6249874969510.209314123066-0.3121825519950.40569362697-0.00971364073610.701324450042-0.150742224265-0.08233575340120.07602711830440.05212679249630.0137786454448-0.110070556544-0.0962737285104-0.0492787922373-4.62484744536E-50.186020764974-0.00904040974062-0.02289116121380.143005859264-0.007744216605950.1795806122430.5552168076-5.887102246058.99586553078
52.45138221556-0.751234230215-1.138353920520.7442586516061.35287718812.51904536640.04560064769741.442780368311.00407829589-1.518750492770.4750475993241.23131741204-0.615564674406-0.2509481121210.7037344007140.572776542327-0.0470894241441-0.2662437687420.4368913242770.1639313708410.42008081240820.14947034843.11569258349-10.4729835711
60.07017947170440.055598788718-0.03014064366320.239505839324-0.3910657573590.46738387683-0.0716180608946-0.03757487471110.07275817365520.0654417459948-0.0212259937778-0.153550964273-0.2025255262730.0601980919583-2.98661075075E-50.227477887318-0.0331598608788-0.03019060983720.173571605577-0.004486882318940.18112135294931.6176953371-3.990028101366.05147285537
71.45786946805-1.01478026159-0.2526644201290.797217911280.5621457494481.629731055830.0390335099846-0.2298629608860.12466696830.04750013167-0.2155034704240.2627251038150.0555232296917-0.2029270008875.88334122267E-60.2187768424510.0183476201996-0.01667102055920.226120386537-0.005153092348440.21920495460722.3480465385-13.523487713712.9866724157
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 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 96 )
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 109 )
7X-RAY DIFFRACTION7chain 'A' and (resid 110 through 124 )

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