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- PDB-2g8q: The crystal structure of RNase A from monoclinic crystals at 100 K -

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Basic information

Entry
Database: PDB / ID: 2g8q
TitleThe crystal structure of RNase A from monoclinic crystals at 100 K
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / RIBONUCLEASE / ENDONUCLEASE
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
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsLeonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: Bioorg.Med.Chem. / Year: 2006
Title: The binding of 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine to ribonuclease A in the crystal.
Authors: Leonidas, D.D. / Maiti, T.K. / Samanta, A. / Dasgupta, S. / Pathak, T. / Zographos, S.E. / Oikonomakos, N.G.
History
DepositionMar 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)27,4172
Polymers27,4172
Non-polymers00
Water6,720373
1
A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.983, 32.551, 72.355
Angle α, β, γ (deg.)90.00, 90.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-174-

HOH

DetailsThe biologically significantly molecule is a monomer.

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 MM SODIUM CITRATE BUFFER AND 20 % PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8068 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2005
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8068 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 37534 / Num. obs: 37534 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 16.14 Å2 / Rsym value: 0.029 / Net I/σ(I): 3.7
Reflection shellResolution: 1.5→1.54 Å / Mean I/σ(I) obs: 3.7 / Num. unique all: 2606 / Rsym value: 0.13 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1AFU

1afu


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.187 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1878 5 %RANDOM
Rwork0.18511 ---
all0.18671 35654 --
obs0.18671 35654 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.02 Å2
2--0.29 Å20 Å2
3----0.46 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å / Luzzati sigma a obs: 0.193 Å
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 0 373 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211953
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9242644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18525.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.577158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021474
X-RAY DIFFRACTIONr_nbd_refined0.1880.2965
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.244
X-RAY DIFFRACTIONr_mcbond_it0.641.51265
X-RAY DIFFRACTIONr_mcangle_it1.06522017
X-RAY DIFFRACTIONr_scbond_it1.6243753
X-RAY DIFFRACTIONr_scangle_it2.5684.5627
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 144 -
Rwork0.2 2606 -
obs-2606 99.71 %
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)
12.50090.10210.06083.44531.76984.86380.13590.12230.1232-0.1892-0.0048-0.1686-0.4114-0.0588-0.13110.0690.00950.0420.02240.0381-0.013330.22818.73249.0486
20.6888-1.96931.109323.5573.15914.0225-0.5411-0.1109-0.43641.59740.0161.71321.0111-0.50070.52510.0821-0.00490.0550.0729-0.04560.041524.8384-5.3717-1.6055
33.4426-1.3131-2.17681.57220.92882.72280.20460.20380.1579-0.27440.0426-0.2249-0.2563-0.0202-0.24720.035-0.0110.03010.04720.0115-0.016632.38362.0714.2962
43.7307-0.01990.60961.5972-0.70752.4661-0.032-0.005-0.04210.06750.0672-0.1109-0.0359-0.2115-0.03520.01170.00480.00180.02060.00780.014628.1081-1.317323.8126
55.61560.3368-3.14171.341-0.1073.2963-0.06040.0373-0.1359-0.20790.1058-0.39060.22520.1737-0.04530.0112-0.01290.03630.0271-0.05170.021637.8775-5.08191.7623
61.75280.50920.21172.26980.41322.1025-0.00590.1257-0.0237-0.0580.0695-0.08240.0424-0.2038-0.06360.0222-0.00310.00770.0390.01490.01428.20570.529816.9756
74.49560.33710.95812.28211.21555.6785-0.09760.40090.1672-0.11710.175-0.0344-0.25180.0192-0.07740.0207-0.01830.01120.06260.0170.017715.714-1.811329.1746
86.8722-4.78863.259912.25120.46042.38360.28381.02780.5714-1.0941-0.497-0.0032-0.28570.69970.21320.09690.0084-0.01350.18340.1264-0.12028.28653.385718.104
94.12610.26340.69161.68610.72531.77670.00860.5384-0.2273-0.2221-0.08190.07420.00910.05440.07330.01560.01030.0050.06520.0056-0.00819.0242-2.891124.8504
103.23890.758-0.77542.36-0.2491.2898-0.0666-0.1007-0.08560.03220.0877-0.01170.087-0.0458-0.0210.0173-0.0058-0.01680.00560.00440.042711.65660.033444.1664
112.20760.78091.4611.09911.23253.0486-0.14560.44070.0605-0.26970.00370.1023-0.11050.06710.14180.03140.0046-0.03530.02330.00840.00212.83742.094824.9972
122.8762-0.76650.40061.7089-0.23941.9625-0.08410.0624-0.0164-0.11050.04020.1216-0.0114-0.02950.04390.0395-0.0192-0.01370.00420.00620.031411.5586-0.41939.6874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 161 - 16
2X-RAY DIFFRACTION2AA17 - 2317 - 23
3X-RAY DIFFRACTION3AA24 - 5624 - 56
4X-RAY DIFFRACTION4AA57 - 7757 - 77
5X-RAY DIFFRACTION5AA78 - 10078 - 100
6X-RAY DIFFRACTION6AA101 - 124101 - 124
7X-RAY DIFFRACTION7BB1 - 201 - 20
8X-RAY DIFFRACTION8BB21 - 3121 - 31
9X-RAY DIFFRACTION9BB32 - 5032 - 50
10X-RAY DIFFRACTION10BB51 - 7451 - 74
11X-RAY DIFFRACTION11BB75 - 10275 - 102
12X-RAY DIFFRACTION12BB103 - 124103 - 124

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