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- PDB-7q7b: Room temperature structure of RNase A at atmospheric pressure in ... -

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Basic information

Entry
Database: PDB / ID: 7q7b
TitleRoom temperature structure of RNase A at atmospheric pressure in a sapphire capillary after high helium gas pressure release
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: 1.78 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 20, 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
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-61 kcal/mol
Surface area6990 Å2
Unit cell
Length a, b, c (Å)64.670, 64.670, 65.220
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.: 67 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
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.

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Data collection

DiffractionMean 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: 1.78→28 Å / Num. obs: 15243 / % possible obs: 98.18 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.18 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1107 / Rpim(I) all: 0.0559 / Net I/σ(I): 7.38
Reflection shellResolution: 1.78→1.844 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.512 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1502 / CC1/2: 0.311 / CC star: 0.689 / Rpim(I) all: 0.8206 / % possible all: 98.55
Cell measurementPressure: 101.325 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: 1.78→28 Å / SU ML: 0.2431 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0547 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1842 1191 7.82 %
Rwork0.1491 14044 -
obs0.1517 15235 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.24 Å2
Refinement stepCycle: LAST / Resolution: 1.78→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 14 67 1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091085
X-RAY DIFFRACTIONf_angle_d1.0551491
X-RAY DIFFRACTIONf_chiral_restr0.053164
X-RAY DIFFRACTIONf_plane_restr0.0071196
X-RAY DIFFRACTIONf_dihedral_angle_d12.4633715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.850.37161340.33981534X-RAY DIFFRACTION98.52
1.85-1.940.2951290.25061538X-RAY DIFFRACTION98.87
1.94-2.040.24361280.20291565X-RAY DIFFRACTION98.6
2.04-2.170.20411320.16691555X-RAY DIFFRACTION99.18
2.17-2.330.20351280.15331545X-RAY DIFFRACTION98.53
2.33-2.570.18771270.14121558X-RAY DIFFRACTION98.65
2.57-2.940.17851340.14611568X-RAY DIFFRACTION98.27
2.94-3.70.16421390.13491556X-RAY DIFFRACTION97.3
3.7-280.15161400.12361625X-RAY DIFFRACTION96.34
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)
10.296657683709-0.406314611373-0.2236349516590.806858171237-0.1100218742151.16545704932-0.0419377014008-0.006126620259580.16004599162-0.1796127662370.1733609031220.3994202466510.00961899531619-0.5560303579615.53247308757E-50.244608315603-0.0366714072636-0.01485669868640.2642140853990.0108757947870.28930774345319.5689428902-15.87806163222.76015781831
20.372627368097-0.1854091958520.2804113233980.5351656155620.166123202370.358775206482-0.01674994826220.234445281098-0.0330772613988-0.332646762625-0.0767352869565-0.565637829204-0.08842914796030.756089924213-0.0002128598412690.38487442257-0.05409709091660.04131497010440.44989556267-0.006392237258380.32562598934535.5135296-9.35476370028-3.44805945942
30.276517131992-0.01411036266310.1916429720050.309179713187-0.1135890384290.242035426531-0.1976738535730.4702855333630.085326805949-0.5843371956570.356896792898-0.2454342620920.2805324722060.132863468062-0.0002734041389270.425376704118-0.0663279328659-0.02450392964180.305827060067-0.0008598212590390.24820288897128.2917535493-7.13483900537-7.45521762376
41.970992059491.82637926846-1.607264777263.423036326770.01991641758782.56339008233-0.2504037776210.4404214608640.138821038751-0.4201143163480.2375247543810.689919026753-0.0189187482912-0.4005866753510.009626825727140.276280226911-0.071656933576-0.06910074640170.2867902558680.0008148486537980.3317003587522.7540686668-7.76360992176-2.37250836151
51.206123604011.490469853960.2934887399892.22422957847-0.3650502247211.80562587307-0.115155521847-0.320005185039-0.004054983478490.205657413746-0.128083984830.2613205945530.0717216870792-0.2883737822810.0001042268741170.2523596170580.0384577510485-0.03394511010630.29519676775-0.03299443198610.28070844919824.9101814988-12.019175710617.240335096
60.6917158845850.431020047225-0.4377941229170.7611233780010.1676467080941.20937556011-0.167937786194-0.1340176726990.03237509126730.08217638312460.0407378689319-0.133117685031-0.1449368164080.0326720030068-1.41790398769E-50.242373197404-0.016145915765-0.01696418127970.220174326059-0.01450406205870.25566234549430.6657856963-5.946561904769.01573252405
70.339957551476-0.04037428167910.1204193241550.01799511743380.03033975941520.168784602199-0.7995870101841.377425761371.50364890538-1.964245606930.6355021499971.67198604351-0.817860613367-0.212261218820.04295773774160.74362264947-0.0792942593213-0.2901131081150.5825081915030.162311929470.65933471653920.14526882873.08250895265-10.2955195708
80.100619417956-0.0531868262645-0.08528217504320.538668518113-0.4732401496470.569814687714-0.0299041688669-0.0808600390940.04561920557770.0523851286561-0.039488005384-0.15240889024-0.3317428164240.171865962392-3.19886029408E-50.306613750536-0.0314273618777-0.03359039306670.277435300289-0.006572777621390.2475712935331.7184125918-4.032596175726.07333121124
90.109063408502-0.01940235089510.0429107042520.1770913248110.1243481976090.313877899662-0.0199610561014-0.193023140312-0.4592943750660.275617428435-0.2383081101080.2069837043940.739685742658-0.6180178454470.0004370009228540.378400987745-0.02736622983380.01814030259080.3644820006180.0255301820960.35909229930720.5671094085-19.484466853714.2863752781
101.443462256570.9276293895720.327426218750.7223350038350.2896977572920.299136918043-0.238079088022-0.8584326445051.29063705174-0.241450659192-0.3253694239830.42136156128-0.7666818989190.0818194432361-0.02249906760440.3502216143770.0838339357754-0.02514545386320.3388762103820.02080461727750.39891261911824.7204954367-6.352312200511.3315845902
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 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 71 )
6X-RAY DIFFRACTION6chain 'A' and (resid 72 through 86 )
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 96 )
8X-RAY DIFFRACTION8chain 'A' and (resid 97 through 109 )
9X-RAY DIFFRACTION9chain 'A' and (resid 110 through 118 )
10X-RAY DIFFRACTION10chain 'A' and (resid 119 through 124 )

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