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- PDB-2qca: A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2... -

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Basic information

Entry
Database: PDB / ID: 2qca
TitleA New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease / Protein-Nucleotide Complex / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for High-Throughput Structural Biology / CHTSB
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
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsLarson, S.B. / Day, J.S. / Cudney, R. / McPherson, A. / Center for High-Throughput Structural Biology (CHTSB)
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.
Authors: Larson, S.B. / Day, J.S. / Cudney, R. / McPherson, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: A novel strategy for the crystallization of proteins: X-ray diffraction validation
Authors: Larson, S.B. / Day, J.S. / Cudney, R. / McPherson, A.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4033
Polymers13,7081
Non-polymers6942
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.080, 55.080, 39.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Pancreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 295 K / pH: 7
Details: Reservoir: 0.6 ml of 30% PEG 3350 in 0.1 M HEPES at pH 7.0. Sample: 2 ul 10-40 mg/ml Protein in 0.1 M HEPES at pH 7.0 and 2 ul of 0.1 M DGP, cholesterol, thymine and oxamic acid in 15% PEG ...Details: Reservoir: 0.6 ml of 30% PEG 3350 in 0.1 M HEPES at pH 7.0. Sample: 2 ul 10-40 mg/ml Protein in 0.1 M HEPES at pH 7.0 and 2 ul of 0.1 M DGP, cholesterol, thymine and oxamic acid in 15% PEG 3350 and 9.1 M HEPES at pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.00

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 8, 2006 / Details: OSMIC MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.33→27.54 Å / Num. obs: 27155 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Biso Wilson estimate: 27.06 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.7
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 1.49 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 0.8 / % possible all: 24.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RNO

1rno


Resolution: 1.33→27.54 Å / Num. parameters: 10604 / Num. restraintsaints: 13217 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: DGP FROM PARKINSON, ET AL., ACTA CRYST. D52(1996)57-64
Stereochemistry target values: ENGH & HUBER
Details: HYDROGEN ATOMS WERE INCLUDED IN RIDING POSITIONS. HYDROGEN ATOMS OF HYDROXYL GROUPS WERE PLACED BY HAND BASED ON BEST HYDROGEN BONDING INTERACTIONS. WATER MOLECULES WERE OBTAINED INITIALLY ...Details: HYDROGEN ATOMS WERE INCLUDED IN RIDING POSITIONS. HYDROGEN ATOMS OF HYDROXYL GROUPS WERE PLACED BY HAND BASED ON BEST HYDROGEN BONDING INTERACTIONS. WATER MOLECULES WERE OBTAINED INITIALLY FOUND FROM AUTOMATIC MAP INTERPRETATION AND LATER FROM MANUAL IDENTIFICATION FROM FO-FC AND 2FO-FC MAPS. WATER OCCUPANCIES WERE INITIALLY SET TO 1.0, BUT REDUCED TO 0.5 IF B VALUES EXCEEDED 80 A^2.
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 2672 11.1 %RANDOM
Rwork0.1194 ---
all0.1253 26810 --
obs0.1253 -79.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228
Displacement parametersBiso mean: 39.6 Å2
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 914 / Occupancy sum non hydrogen: 1105.57
FreeObs
Luzzati coordinate error0.17 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.33→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 46 137 1134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0.091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.33-1.380.403690.396X-RAY DIFFRACTION1022.37
1.38-1.440.3592170.33X-RAY DIFFRACTION1067.87
1.44-1.50.2962890.25X-RAY DIFFRACTION1097.81
1.5-1.580.2393160.188X-RAY DIFFRACTION1099.83
1.58-1.680.1873050.15X-RAY DIFFRACTION1099.84
1.68-1.810.1732930.118X-RAY DIFFRACTION1099.8
1.81-1.990.1612830.095X-RAY DIFFRACTION1099.97
1.99-2.280.1542990.086X-RAY DIFFRACTION1099.87
2.28-2.980.1513080.086X-RAY DIFFRACTION1099.9
2.87-29.1610.1882930.13X-RAY DIFFRACTION1097.74

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