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- PDB-1fut: CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ... -

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Basic information

Entry
Database: PDB / ID: 1fut
TitleCRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP
ComponentsRIBONUCLEASE F1
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / : / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-2'-MONOPHOSPHATE / Guanyl-specific ribonuclease F1
Similarity search - Component
Biological speciesGibberella fujikuroi (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKatayanagi, K. / Vassylyev, D.G. / Ishikawa, K. / Morikawa, K.
CitationJournal: J.Mol.Biol. / Year: 1993
Title: Crystal structures of ribonuclease F1 of Fusarium moniliforme in its free form and in complex with 2'GMP.
Authors: Vassylyev, D.G. / Katayanagi, K. / Ishikawa, K. / Tsujimoto-Hirano, M. / Danno, M. / Pahler, A. / Matsumoto, O. / Matsushima, M. / Yoshida, H. / Morikawa, K.
History
DepositionJan 18, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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 F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3532
Polymers10,9901
Non-polymers3631
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.160, 40.160, 120.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: RESIDUES 39 AND 55 ARE CIS PROLINES.

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Components

#1: Protein RIBONUCLEASE F1


Mass: 10989.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella fujikuroi (fungus) / References: UniProt: P10282, EC: 3.1.27.3
#2: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: RFN1_FUSMO SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 32 THR 32 THR 36 SER 36

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 3.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
230 mMNa citrate1drop
320 %(v/v)MPD1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. obs: 5602 / Rmerge(I) obs: 0.07

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→6 Å / Rfactor obs: 0.168 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 24 46 843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8461.5
X-RAY DIFFRACTIONp_mcangle_it1.4042
X-RAY DIFFRACTIONp_scbond_it1.7392
X-RAY DIFFRACTIONp_scangle_it2.7262.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1560.15
X-RAY DIFFRACTIONp_singtor_nbd0.160.3
X-RAY DIFFRACTIONp_multtor_nbd0.1960.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2140.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.32
X-RAY DIFFRACTIONp_staggered_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor21.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 5331 / σ(F): 1 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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