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- PDB-7q79: Room temperature structure of RNase A at 100 MPa helium gas press... -

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Basic information

Entry
Database: PDB / ID: 7q79
TitleRoom temperature structure of RNase A at 100 MPa helium gas pressure in a sapphire capillary
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
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 / lyase activity / defense response to Gram-positive bacterium / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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

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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
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-60 kcal/mol
Surface area7050 Å2
Unit cell
Length a, b, c (Å)64.400, 64.400, 64.750
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 / Pancreatic ribonuclease family / 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 (cattle) / Gene: RNASE1, RNS1 / Production host: Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.5 %
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: 100000 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: 1.55→28 Å / Num. obs: 22676 / % possible obs: 98.73 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.53 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1619 / Rpim(I) all: 0.064 / Net I/σ(I): 6.11
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.905 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2245 / CC1/2: 0.306 / CC star: 0.685 / Rpim(I) all: 0.7833 / % possible all: 99.6
Cell measurementPressure: 100000 kPa

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Processing

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

2e3w


Resolution: 1.55→28 Å / SU ML: 0.2113 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8459 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1878 1780 7.85 %
Rwork0.1558 20893 -
obs0.1582 22673 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.88 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 14 80 1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961092
X-RAY DIFFRACTIONf_angle_d1.04451501
X-RAY DIFFRACTIONf_chiral_restr0.0545165
X-RAY DIFFRACTIONf_plane_restr0.0069197
X-RAY DIFFRACTIONf_dihedral_angle_d11.9049723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.37971350.32151586X-RAY DIFFRACTION99.54
1.59-1.640.31261350.29341600X-RAY DIFFRACTION99.6
1.64-1.690.2821410.26441588X-RAY DIFFRACTION99.2
1.69-1.750.27161290.24411592X-RAY DIFFRACTION98.91
1.75-1.820.27731390.21471600X-RAY DIFFRACTION99.2
1.82-1.910.24841320.17861584X-RAY DIFFRACTION98.73
1.91-2.010.18731420.15041608X-RAY DIFFRACTION99.26
2.01-2.130.17211280.1371596X-RAY DIFFRACTION99.08
2.13-2.30.15611350.13751609X-RAY DIFFRACTION98.7
2.3-2.530.1741350.14181623X-RAY DIFFRACTION98.6
2.53-2.890.18961380.15061611X-RAY DIFFRACTION98.54
2.89-3.640.16591450.14351616X-RAY DIFFRACTION97.62
3.64-280.1591460.13071680X-RAY DIFFRACTION96.97
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)
10.202902234666-0.223492884128-0.1780813326230.694398080388-0.2500160231630.8644094298450.0216152695190.002661417594740.112116626430.01047789775020.112496981290.322134616989-0.0315261551637-0.4851421716060.000167914514250.195419990031-0.0308622296118-0.001400433633450.202541650650.00569040751780.21293700372619.4912922913-15.78428143792.80297082724
20.293728561103-0.3351708316670.1060084659370.457556013057-0.04086294544790.1197527110920.02402088094360.1945756171220.0786179460867-0.204010989033-0.109466716894-0.56168311468-0.2715285831530.587450196910.0004229983301980.314555075228-0.04453854150730.04773648965710.3519906912870.00914855844960.28027085583235.4244724192-9.33853800289-3.41413098353
30.1488866779960.1142547205140.08631171917260.293513332276-0.03468015379220.159021751447-0.09644391109760.349026196526-0.164142372821-0.6766790492350.250910952942-0.1782462390260.2536579863610.082151508124-0.0005972630816950.349516133036-0.0593355989573-0.01812964108850.233442680349-0.01039277122660.178095384627.9219555122-7.25558327935-7.81537832275
41.361948371211.21217504051-1.170130781772.628008157890.1310776173851.89177023683-0.1336024970240.1688193870780.129890113705-0.3495976439090.1270695608020.5379570212180.006669023843-0.3983533016350.01171528468290.226654832255-0.0458615785407-0.06842518001650.217720594164-0.004646201810620.26258412254122.6796963678-7.80984954132-2.40735368763
51.426970937651.577523663220.4071052465541.91585396699-0.03180315759881.70913474291-0.0791561997494-0.2051539922060.1550114656470.168864934668-0.06168136832970.2382904014540.032218879456-0.305568580114-9.38685870495E-60.2154669413550.0332754551622-0.02939185815350.232788128307-0.02545566424240.22036605226124.846261588-11.903376923717.1424937095
60.4935246234410.369113917357-0.1741181922490.308610370838-0.1912404771480.888779190097-0.12778962649-0.06543912692650.03924467421640.07388972221040.0173377779347-0.0841891169664-0.0864108282487-0.0241407714803-0.0001612306259190.208169428309-0.00789219508049-0.02217256512290.176236873525-0.01181150442740.1988138365630.5396524036-5.888147020768.97375588452
70.307475022983-0.146158870737-0.412026086590.06921706993940.1958376941890.552495150362-0.4893405960471.219277358171.12813209719-1.456397083320.5083033993911.33476949922-0.768630720526-0.2868960262760.1497799190040.582672183995-0.0472527412665-0.240679844310.425732962480.1285564122190.50716224236520.095335832.96117228944-10.6021452397
80.01619793705730.0787702218343-0.09380385178560.36580653464-0.4374999381190.519964796327-0.0644003299945-0.03590881454160.0578740673150.0318945895801-0.0107423852742-0.143073963157-0.1496259886620.0763306816829.13369605085E-50.242602123524-0.0282935707195-0.02737543306980.182599304616-0.001666527165910.19299742398431.6265225416-3.972652475116.01926433743
90.192753933737-0.0739414457246-0.0418782010580.1686590833950.121462192730.2932240791280.119878190501-0.225394744967-0.3593663756740.140498223144-0.2065247851190.2357955127980.573074780142-0.4510878959480.0003758667974820.292241183957-0.02227571652-0.001248339236810.2844591899140.01783000811120.27077039073220.4798407874-19.347471009714.2766109668
100.6480664554750.2322061350120.1874458911290.1623056324910.1405745861890.31148465111-0.424680815056-0.3747013115741.35830325236-0.274626054085-0.05953675818550.557820171244-0.5863283516130.0672819692572-0.01185972236320.2728181275670.0650815579307-0.04401472088750.250746241670.01141496937060.31275214899424.6616338866-6.2231705778611.3023299096
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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