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- PDB-1qhc: CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-PHOSPHO-2'... -

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Basic information

Entry
Database: PDB / ID: 1qhc
TitleCRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-PHOSPHO-2'-DEOXYURIDINE-3'-PYROPHOSPHATE ADENOSINE-3'-PHOSPHATE
ComponentsPROTEIN (RIBONUCLEASE A)
KeywordsHYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / 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-PUA / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLeonidas, D.D. / Acharya, K.R.
Citation
Journal: Biochemistry / Year: 1999
Title: Toward rational design of ribonuclease inhibitors: high-resolution crystal structure of a ribonuclease A complex with a potent 3',5'-pyrophosphate-linked dinucleotide inhibitor.
Authors: Leonidas, D.D. / Shapiro, R. / Irons, L.I. / Russo, N. / Acharya, K.R.
#1: Journal: Biochemistry / Year: 1997
Title: Crystal Structures of Ribonuclease A Complexes with 5'-Diphosphoadenosine 3'- Phosphate and 5'-Diphosphoadenosine 2'-Phosphate at 1.7 A Resolution
Authors: Leonidas, D.D. / Shapiro, R. / Irons, L.I. / Russo, N. / Acharya, K.R.
History
DepositionMay 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RIBONUCLEASE A)
B: PROTEIN (RIBONUCLEASE A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0114
Polymers27,4172
Non-polymers1,5952
Water2,468137
1
A: PROTEIN (RIBONUCLEASE A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5062
Polymers13,7081
Non-polymers7971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RIBONUCLEASE A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5062
Polymers13,7081
Non-polymers7971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.360, 33.210, 73.060
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.574776, 0.784184, 0.233854), (-0.817028, -0.565936, -0.11037), (0.045796, -0.254504, 0.965987)
Vector: 27.068, -17.904, -278.129)

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Components

#1: Protein PROTEIN (RIBONUCLEASE A) / EC 3.1.27.5


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-PUA / ADENYLATE-3'-PHOSPHATE-[[2'-DEOXY-URIDINE-5'-PHOSPHATE]-3'-PHOSPHATE] / U-PI-A-PI


Mass: 797.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N7O20P4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details1AFK A SWS P00656 1 - 26 NOT IN ATOMS LIST 1AFK B SWS P00656 1 - 26 NOT IN ATOMS LIST

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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: 2.2 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: CRYSTALLIZED FROM 20% PEG 4000, 20 MM SODIUM CITRATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 16 ℃ / Details: Leonidas, D.D., (1997) Biochemistry, 36, 5578.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMsodium citrate1drop
310 %PEG40001drop
420 %PEG40001reservoir
520 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 25723 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.083 / Net I/σ(I): 5.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.05 / Rsym value: 0.326 / % possible all: 84

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFK

1afk


Resolution: 1.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1295 5 %RANDOM
Rwork0.2 ---
obs-25665 94.3 %-
Displacement parametersBiso mean: 32.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 100 137 2139
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.82
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.521.5
X-RAY DIFFRACTIONx_mcangle_it2.552
X-RAY DIFFRACTIONx_scbond_it2.792
X-RAY DIFFRACTIONx_scangle_it4.62.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 180 4.9 %
Rwork0.374 3527 -
obs--82.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.82
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.386 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.374

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