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- PDB-2oqf: Structure of a synthetic, non-natural analogue of RNase A: [N71K(... -

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Basic information

Entry
Database: PDB / ID: 2oqf
TitleStructure of a synthetic, non-natural analogue of RNase A: [N71K(Ade), D83A]RNase A
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / non-natural amino acid
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
Ribonuclease pancreatic
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBoerema, D.J. / Tereshko, V.A. / Zhang, J.L. / He, C. / Kent, S.B.H.
CitationJournal: To be Published
Title: Design, Synthesis, and Characterization of Non-natural RNase A Analogues with Enhanced Second-step Catalytic Activity
Authors: Boerema, D.J. / Tereshko, V.A. / Zhang, J.L. / He, C. / Kent, S.B.H.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
C: Ribonuclease pancreatic
D: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)55,1864
Polymers55,1864
Non-polymers00
Water1,63991
1
A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7961
Polymers13,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7961
Polymers13,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7961
Polymers13,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7961
Polymers13,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.578, 50.534, 62.863
Angle α, β, γ (deg.)85.26, 74.31, 82.70
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
12B
22D
32B
42D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSCYSCYSAA1 - 651 - 65
211LYSLYSCYSCYSCC1 - 651 - 65
321SERSERALAALAAA75 - 12275 - 122
421SERSERALAALACC75 - 12275 - 122
112LYSLYSCYSCYSBB1 - 651 - 65
212LYSLYSCYSCYSDD1 - 651 - 65
322SERSERALAALABB75 - 12275 - 122
422SERSERALAALADD75 - 12275 - 122

NCS ensembles :
ID
1
2

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Components

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


Mass: 13796.482 Da / Num. of mol.: 4 / Mutation: N71K(Ade), D83A / Source method: obtained synthetically
Details: Combined solid phase peptide synthesis and native chemical ligation chemistries.
References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.1 Å3/Da / Density % sol: 41.51 %

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97985
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19122

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NUI

2nui


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.871 / SU B: 27.699 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.901 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2912 1958 10.3 %RANDOM
Rwork0.22927 ---
obs0.23555 17142 97.56 %-
all-19122 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.489 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.02 Å21.34 Å2
2---1.78 Å21.1 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 0 91 3909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193919
X-RAY DIFFRACTIONr_bond_other_d0.0010.023247
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9015300
X-RAY DIFFRACTIONr_angle_other_deg0.7522.147670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47924.941170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6741516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
X-RAY DIFFRACTIONr_nbd_refined0.1890.2658
X-RAY DIFFRACTIONr_nbd_other0.1880.23113
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21895
X-RAY DIFFRACTIONr_nbtor_other0.0850.21843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1460.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3281.53175
X-RAY DIFFRACTIONr_mcbond_other0.0451.5992
X-RAY DIFFRACTIONr_mcangle_it0.38123995
X-RAY DIFFRACTIONr_scbond_it0.59531713
X-RAY DIFFRACTIONr_scangle_it0.9074.51305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 1598 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.220.5
2Bmedium positional0.180.5
1Amedium thermal0.172
2Bmedium thermal0.162
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 133 -
Rwork0.293 1195 -
obs--92.48 %
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)
12.2632-0.869-0.92312.28070.91.1805-0.0546-0.0216-0.0330.00640.0636-0.04530.09440.0109-0.0089-0.1065-0.0112-0.0259-0.07260.009-0.1067-9.0636-18.61322.6238
22.3925-1.1039-0.55122.53280.29951.6945-0.11890.0973-0.04290.06770.0850.10680.0558-0.10670.0339-0.0898-0.039-0.0415-0.0410.0261-0.0736-1.2056-4.9497.7585
30.61170.02370.73642.4374-1.92693.52220.01610.00570.0454-0.03680.06020.0117-0.1628-0.0878-0.0764-0.082-0.00910.0178-0.0582-0.0254-0.03834.172218.8643-8.614
41.7237-0.45770.45922.9032-1.15623.27820.0226-0.01780.02410.28560.0194-0.0243-0.04190.1173-0.042-0.0649-0.00460.0184-0.0579-0.0315-0.05156.55423.5674-23.9983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1241 - 124
2X-RAY DIFFRACTION1AE125 - 1441 - 20
3X-RAY DIFFRACTION2BB1 - 1241 - 124
4X-RAY DIFFRACTION2BF125 - 1541 - 30
5X-RAY DIFFRACTION3CC1 - 1241 - 124
6X-RAY DIFFRACTION3CG125 - 1441 - 20
7X-RAY DIFFRACTION4DD1 - 1211 - 121
8X-RAY DIFFRACTION4DH125 - 1451 - 21

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