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- PDB-7q78: Room temperature structure of RNase A at 72 MPa helium gas pressu... -

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Basic information

Entry
Database: PDB / ID: 7q78
TitleRoom temperature structure of RNase A at 72 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: 1.52 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 area6970 Å2
Unit cell
Length a, b, c (Å)64.280, 64.280, 65.020
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: 56.52 %
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: 72000 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: 1.52→27.83 Å / Num. obs: 24342 / % possible obs: 99.93 % / Redundancy: 8.8 % / Biso Wilson estimate: 19.94 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1495 / Rpim(I) all: 0.0519 / Net I/σ(I): 8.24
Reflection shellResolution: 1.52→1.574 Å / Rmerge(I) obs: 2.602 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 2416 / CC1/2: 0.327 / CC star: 0.702 / Rpim(I) all: 0.917 / % possible all: 99.92
Cell measurementPressure: 72000 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: 1.52→27.83 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6066 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1826 1916 7.87 %
Rwork0.1533 22423 -
obs0.1556 24339 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.96 Å2
Refinement stepCycle: LAST / Resolution: 1.52→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 14 80 1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511072
X-RAY DIFFRACTIONf_angle_d1.29331470
X-RAY DIFFRACTIONf_chiral_restr0.0662162
X-RAY DIFFRACTIONf_plane_restr0.0087192
X-RAY DIFFRACTIONf_dihedral_angle_d11.7054702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.36451350.31511569X-RAY DIFFRACTION99.88
1.56-1.60.29921390.28321588X-RAY DIFFRACTION99.88
1.6-1.650.27221370.26541570X-RAY DIFFRACTION100
1.65-1.70.27191360.23511578X-RAY DIFFRACTION100
1.7-1.760.2231330.20811584X-RAY DIFFRACTION100
1.76-1.830.22851370.18841588X-RAY DIFFRACTION100
1.83-1.920.2131320.16951585X-RAY DIFFRACTION100
1.92-2.020.17091380.13681600X-RAY DIFFRACTION100
2.02-2.140.16231330.12631608X-RAY DIFFRACTION100
2.14-2.310.15271340.13421592X-RAY DIFFRACTION99.88
2.31-2.540.17991340.14131607X-RAY DIFFRACTION99.94
2.54-2.910.19551380.15031613X-RAY DIFFRACTION100
2.91-3.660.15041450.14071626X-RAY DIFFRACTION99.94
3.66-27.830.16061450.13081715X-RAY DIFFRACTION99.89
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)
10.120815207854-0.134541778852-0.1286951718080.692716894624-0.1025160916610.715532962036-0.006187006628810.005113140395180.154724858651-0.1471158101130.03299275662630.345014569588-0.0354594662391-0.410890311189-0.000143946777470.184214000133-0.0320507982481-0.008887063882980.1773231257320.0005367964706120.20448038988219.467268454-15.73198672932.74653736
20.368958764087-0.2670880490310.2392441665050.5186475265490.1325481928780.329148032888-0.04346617026960.2281896297660.0206173256399-0.276344967771-0.0430922437756-0.535132852827-0.2662772654960.5698603067940.0007723070834350.288589202712-0.05328553671690.04264189006250.3342831142310.000438634398130.24684361597235.550154231-9.5872478947-2.97467313276
30.2015337272450.04589763613290.04441688757710.677924309951-0.08325621938840.131846412935-0.1227885616930.42303011414-0.077923550667-0.7216790729260.257674088587-0.2343938938380.2044082863870.113641623625-0.0004688939566930.312034030598-0.0638635965788-0.0147699461540.207007980898-0.007661259005380.17309279782428.1652509669-7.05437254465-7.45841240548
41.283146481731.29727336346-0.9623998715432.857852009830.2300248091661.57780700767-0.2345440166140.1910369379710.0882960515414-0.3280844709160.169733857020.488098200588-0.0524438162926-0.3445267044740.01139436649260.210150679356-0.0438601257038-0.058401055620.1964276486350.0002513601246410.2366508146522.6542563554-7.75731547101-2.42243353222
51.190898563271.251869581350.1720056702351.46391685060.04616358298451.37947959779-0.0549836462616-0.118602532260.09233517883710.0728984122247-0.08446681136840.1943404417220.0147453716758-0.308683233293-8.09804260694E-50.2115636395130.0282221821421-0.03092796603770.208553343099-0.01862673485520.19545149532425.1863022865-12.012613026617.0203274934
60.6320904627930.404193080763-0.2289596393040.2824478684950.02016262983170.7681861309-0.139206694292-0.07288588022620.0449505649910.04842979150090.0319452778208-0.0896820459786-0.0779345201044-0.06252639818348.92239293505E-50.20069508312-0.00123960254656-0.02022580264280.150059641312-0.007008200021840.18693519256830.4875010951-5.851940898688.96577046404
72.18288005187-0.341355980725-0.1628540259830.4401521884951.060546592842.78375709053-0.2479268207391.260949074811.08146348153-1.358873181880.3955311080361.24024891588-0.640366649085-0.2934585501710.69003694590.552628309749-0.0453062088631-0.2397685215190.4076529698730.1374192608570.42398053799720.10055289633.1152141754-10.4918428618
80.08550164141370.131981186327-0.106231575360.281877394747-0.3410724692810.443127562309-0.03859840514990.003947928539230.01244355639350.031495521482-0.0252610810911-0.1062656464-0.1688664397040.08233457331740.000142405558210.233811428914-0.0246697644069-0.02942971409180.1746602589680.001039373420460.19186948439231.5642903679-3.950734466996.02103164016
90.138499855233-0.09137540940790.01578650257870.2234129524870.1951108103670.3670337116880.0510723443245-0.125110011751-0.22016627710.104189759821-0.2392964918770.3723310963430.691634587-0.518119186535-0.00432475416470.299856434701-0.04033306261230.01161111715980.259919034504-0.00410713471460.24657651668320.4597576573-19.362187050814.2428852201
100.4832755237990.0537347740914-0.01034522953970.1037016639610.02831762961740.270425185272-0.167239699714-0.4294997866050.829198409748-0.179183956757-0.2135523995450.268641544533-0.499943196481-0.0240500338999-1.13463153398E-50.2541173551460.050112113349-0.04293161024460.248778847621-0.005425350494660.26658219942724.6159505459-6.207137316911.2686108828
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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