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- PDB-2g8r: The crystal structure of the RNase A- 3-N-piperidine-4-carboxyl-3... -

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Basic information

Entry
Database: PDB / ID: 2g8r
TitleThe crystal structure of the RNase A- 3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine complex
ComponentsRibonuclease pancreatic
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
Chem-N3E / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1274
Polymers27,4172
Non-polymers7112
Water4,720262
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4193
Polymers13,7081
Non-polymers7112
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)100.174, 32.530, 72.512
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biologically significant assembly is a monomer

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Components

#1: Protein Ribonuclease pancreatic / 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: Chemical ChemComp-N3E / 1-[3-(4-CARBOXYPIPERIDIN-1-YL)-3-DEOXY-BETA-D-ARABINOFURANOSYL]PYRIMIDINE-2,4(1H,3H)-DIONE / 3-N-PIPERIDINE-4-CARBOXYL-3-DEOXY-ARA-URIDINE


Mass: 355.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N3O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 42.89 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20mM 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: 1.7→30 Å / Num. all: 24227 / Num. obs: 24227 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.5 % / Biso Wilson estimate: 23.58 Å2 / Rsym value: 0.071 / Net I/σ(I): 4.5
Reflection shellResolution: 1.7→1.75 Å / Mean I/σ(I) obs: 3.2 / Num. unique all: 1442 / Rsym value: 0.45 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2G8Q

2g8q


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.483 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23035 1304 5.1 %RANDOM
Rwork0.19057 ---
all0.19266 24225 --
obs0.19266 24225 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.984 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.22 Å2
2---0.01 Å20 Å2
3----0.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.241 Å / Luzzati sigma a obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 50 262 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212008
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9532723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71225.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.518158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021510
X-RAY DIFFRACTIONr_nbd_refined0.1920.2975
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.230
X-RAY DIFFRACTIONr_mcbond_it0.6041.51272
X-RAY DIFFRACTIONr_mcangle_it0.95522015
X-RAY DIFFRACTIONr_scbond_it1.5393819
X-RAY DIFFRACTIONr_scangle_it2.4014.5708
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 75 -
Rwork0.286 1442 -
obs-1442 98.7 %
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)
11.61440.30990.23914.94630.78928.54750.3321-0.2165-0.26320.1255-0.0666-0.36910.6995-0.0896-0.26550.0662-0.0342-0.07320.00430.05430.010130.3441-8.252227.3282
226.189431.322518.560577.4730.013725.4543-2.3931-0.3249-0.1934-3.35890.7295-1.6919-0.5092-0.02961.66360.10840.07430.01130.1410.02070.10324.5215.705738.1208
37.4673-0.69211.67516.51622.29715.81050.4344-0.6102-0.30360.5626-0.0113-0.7040.5259-0.0982-0.42310.0933-0.0486-0.13830.02810.0488-0.026936.6303-2.691736.8413
42.10150.11381.83441.7373-0.14883.80450.0773-0.2127-0.02850.15240.0415-0.06830.1053-0.2554-0.11880.0039-0.00420.00570.05370.01750.007926.4686-0.375624.0339
55.14160.2906-0.35471.9494-0.10092.2908-0.07260.1786-0.0952-0.1260.0189-0.21080.0352-0.14290.05360.01910.00120.0144-0.00490.01560.031630.23461.886411.6927
612.0992-1.91776.59461.459-1.06446.9798-0.3394-0.36360.21030.38680.2139-0.3965-0.52640.14740.12550.0248-0.0011-0.0598-0.0019-0.05760.010337.29584.829433.8032
72.2119-0.70342.57580.5314-0.24597.2631-0.0902-0.40150.26420.1860.0344-0.2235-0.6839-0.5260.05580.03650.0277-0.0105-0.0025-0.03-0.025629.95798.074129.1278
83.36491.68110.2615.62681.9383.1920.0593-0.0878-0.09720.0307-0.0278-0.0820.0782-0.2185-0.03150.0251-0.0035-0.0031-0.00290.02190.030629.5231-3.941817.1096
94.1171-0.2457-0.0311.52640.32317.5036-0.1659-0.28960.245-0.01180.2884-0.0308-0.32270.2573-0.12250.00530.0065-0.00270.0232-0.02620.025516.38815.66955.7969
1072.46611.1529-23.309611.9246-9.949411.46270.7862-1.2721-4.18171.2902-1.3672-0.07360.14151.06220.5810.1939-0.0109-0.02910.11780.10370.085211.9294-10.196113.5038
118.54870.2033-0.003913.82562.8620.5927-0.1069-0.8501-0.47091.0636-0.0296-0.03190.29590.36260.13640.09920.07690.03340.09550.0951-0.09568.268-2.495717.4846
1219.0399-7.0454-8.29928.35345.53886.00010.0214-0.53361.12390.3982-0.0864-0.0922-0.23690.15650.0649-0.0005-0.004-0.04090.0531-0.0484-0.016710.08157.842316.1626
131.6226-0.3721-0.83831.28781.19751.6355-0.0517-0.1447-0.09270.15560.0296-0.03040.11310.03380.02210.00890.0157-0.0088-0.01150.01220.058512.9958-2.55182.2525
147.7185-4.7696-1.224210.43421.82563.6210.01440.22620.3735-0.052-0.16370.0933-0.1154-0.09050.14930.00140.0167-0.02760.01590.04020.09356.63824.5465-10.69
151.0024-0.26450.0421.03730.6850.6883-0.1213-0.0757-0.14330.1524-0.03990.05570.1696-0.09720.16120.02550.00820.0258-0.01870.01360.05896.0099-3.47942.0285
161.80.0519-0.88010.5103-0.0792.03550.0013-0.20570.0010.1856-0.03550.06440.0138-0.08280.03410.04340.00450.01480.01290.00280.06768.08990.96184.1402
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 - 3924 - 39
4X-RAY DIFFRACTION4AA40 - 6140 - 61
5X-RAY DIFFRACTION5AA62 - 7662 - 76
6X-RAY DIFFRACTION6AA77 - 9577 - 95
7X-RAY DIFFRACTION7AA96 - 10796 - 107
8X-RAY DIFFRACTION8AA108 - 124108 - 124
9X-RAY DIFFRACTION9BB1 - 141 - 14
10X-RAY DIFFRACTION10BB15 - 2315 - 23
11X-RAY DIFFRACTION11BB24 - 3024 - 30
12X-RAY DIFFRACTION12BB31 - 3931 - 39
13X-RAY DIFFRACTION13BB40 - 6040 - 60
14X-RAY DIFFRACTION14BB61 - 7061 - 70
15X-RAY DIFFRACTION15BB71 - 8971 - 89
16X-RAY DIFFRACTION16BB90 - 12490 - 124

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