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- PDB-5jmg: X-ray structure of the complex between bovine pancreatic ribonucl... -

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Basic information

Entry
Database: PDB / ID: 5jmg
TitleX-ray structure of the complex between bovine pancreatic ribonuclease and pentachlorocarbonyliridate(III) (4 days of soaking)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / iridium compound / CORM / protein iridium interaction
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
CARBON MONOXIDE / : / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCaterino, M. / Petruk, A.A. / Vergara, A. / Ferraro, G. / Merlino, A.
CitationJournal: Dalton Trans / Year: 2016
Title: Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules.
Authors: Caterino, M. / Petruk, A.A. / Vergara, A. / Ferraro, G. / Marasco, D. / Doctorovich, F. / Estrin, D.A. / Merlino, A.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,63915
Polymers27,4172
Non-polymers1,22213
Water4,414245
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6049
Polymers13,7081
Non-polymers8968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0356
Polymers13,7081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.932, 32.652, 72.273
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 124 / Label seq-ID: 1 - 124

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ir
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K, 10 mM sodium citrate pH 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→72.27 Å / Num. obs: 19871 / % possible obs: 97.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 2.15
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.3 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
CrystalCleardata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JVT

1jvt


Resolution: 1.85→72.27 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.448 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 1017 5.1 %RANDOM
Rwork0.17273 ---
obs0.1754 18853 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.475 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.2 Å2
2--0.07 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.85→72.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 16 245 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192030
X-RAY DIFFRACTIONr_bond_other_d0.0090.021831
X-RAY DIFFRACTIONr_angle_refined_deg2.3731.9422779
X-RAY DIFFRACTIONr_angle_other_deg1.52834251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29125.05493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86815355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.235159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022384
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02476
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_it2.7022.4821030
X-RAY DIFFRACTIONr_mcbond_other2.6982.481026
X-RAY DIFFRACTIONr_mcangle_it4.0013.7041294
X-RAY DIFFRACTIONr_mcangle_other4.0033.7041293
X-RAY DIFFRACTIONr_scbond_it2.9052.6631000
X-RAY DIFFRACTIONr_scbond_other2.9042.6631000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4513.8821480
X-RAY DIFFRACTIONr_long_range_B_refined7.2520.4042481
X-RAY DIFFRACTIONr_long_range_B_other7.00219.9092353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13270 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 88 -
Rwork0.251 1291 -
obs--91.87 %

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