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- PDB-1z6s: Ribonuclease A- AMP complex -

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Basic information

Entry
Database: PDB / ID: 1z6s
TitleRibonuclease A- AMP complex
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / RIBONUCLEASE
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
ADENOSINE MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsHatzopoulos, G.N. / Leonidas, D.D. / Kardakaris, R. / Kobe, J. / Oikonomakos, N.G.
CitationJournal: Febs J. / Year: 2005
Title: The binding of IMP to Ribonuclease A
Authors: Hatzopoulos, G.N. / Leonidas, D.D. / Kardakaris, R. / Kobe, J. / Oikonomakos, N.G.
History
DepositionMar 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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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)28,1114
Polymers27,4172
Non-polymers6942
Water5,945330
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0562
Polymers13,7081
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0562
Polymers13,7081
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.330, 32.609, 72.419
Angle α, β, γ (deg.)90.00, 90.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1148-

HOH

21B-1170-

HOH

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Components

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


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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.4 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium citrate, PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.8115 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8115 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 37131 / Num. obs: 35273 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.041 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.34 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.064 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23148 1852 5 %RANDOM
Rwork0.19313 ---
all0.19502 35273 --
obs0.19502 35273 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.293 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.01 Å2
2--0.15 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 46 330 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212006
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9642727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71225.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18815336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.369158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021499
X-RAY DIFFRACTIONr_nbd_refined0.2020.2928
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21385
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.239
X-RAY DIFFRACTIONr_mcbond_it0.7181.51265
X-RAY DIFFRACTIONr_mcangle_it1.16222008
X-RAY DIFFRACTIONr_scbond_it2.0543835
X-RAY DIFFRACTIONr_scangle_it3.2114.5719
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 148 -
Rwork0.24 2587 -
obs-2587 99.13 %
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)
11.7534-0.0189-0.64961.4734-0.0724.33770.03150.2976-0.0479-0.16240.071-0.1574-0.1306-0.0592-0.1025-0.1547-0.00740.0159-0.1368-0.0072-0.135131.29580.38439.9726
22.35660.08450.97871.62080.84462.6418-0.09510.31540.0413-0.31580.02740.1493-0.0683-0.02470.0677-0.1129-0.0279-0.0263-0.12830.0167-0.10379.2056-0.044131.1226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1241 - 124
2X-RAY DIFFRACTION2BB1 - 1241 - 124

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