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- PDB-2w5k: RNASE A-NADPH COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2w5k
TitleRNASE A-NADPH COMPLEX
ComponentsRIBONUCLEASE PANCREATICPancreatic ribonuclease family
KeywordsHYDROLASE / GLYCOPROTEIN / ENDONUCLEASE / INHIBITOR / NUCLEOTIDE / ATP / ENZYME / NUCLEASE / SECRETED / GLYCATION
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-NDP / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChavali, G.B. / Holloway, D.E. / Baker, M.D. / Acharya, K.R.
CitationJournal: Biopolymers / Year: 2009
Title: Influence of Naturally-Occurring 5'-Pyrophosphate-Linked Substituents on the Binding of Adenylic Inhibitors to Ribonuclease A: An X-Ray Crystallographic Study.
Authors: Holloway, D.E. / Chavali, G.B. / Leonidas, D.D. / Baker, M.D. / Acharya, K.R.
History
DepositionDec 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)28,9074
Polymers27,4172
Non-polymers1,4912
Water3,081171
1
A: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4542
Polymers13,7081
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4542
Polymers13,7081
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.962, 33.723, 74.145
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RIBONUCLEASE PANCREATIC / Pancreatic ribonuclease family / RNASE 1 / RNASE A / RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SIGMA CHEMICAL CO. / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NADPH) (NDP): LIGAND IS ONLY PARTIALLY ORDERED

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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: 48 % / Description: NONE
Crystal growpH: 5.5 / Details: 20% PEG 4000, 0.02M SODIUM CITRATE BUFFER, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 17, 2001 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 27237 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.07 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 26.6
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 8.1 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFU

1afu


Resolution: 1.7→74.12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.682 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAIN ATOMS HAVE BEEN OMITTED. RESIDUES 16-24 AND 87-90 OF EACH CHAIN HAVE POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1379 5.1 %RANDOM
Rwork0.176 ---
obs0.177 25858 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-0.02 Å2
2--0.52 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 54 171 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9612743
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55125.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43415346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.994158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.34221242
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.41832019
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8876777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5128724
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.205 96
Rwork0.199 1805

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