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- PDB-3syu: Re-refined coordinates for pdb entry 1det - ribonuclease T1 carbo... -

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Basic information

Entry
Database: PDB / ID: 3syu
TitleRe-refined coordinates for pdb entry 1det - ribonuclease T1 carboxymethylated at GLU 58 in complex with 2'GMP
ComponentsGuanyl-specific ribonuclease T1
KeywordsHYDROLASE / ENDORIBONUCLEASE
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 / ribonuclease T1 activity / cell septum / 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 T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / RE-REFINEMENT / Resolution: 1.95 Å
AuthorsSmart, O.S. / Womack, T.O. / Bricogne, G.
CitationJournal: Biochemistry / Year: 1996
Title: Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP.
Authors: Ishikawa, K. / Suzuki, E. / Tanokura, M. / Takahashi, K.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 0THIS ENTRY 3SYU REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA IN 1DET. ORIGINAL DATA DETERMINED BY ...THIS ENTRY 3SYU REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA IN 1DET. ORIGINAL DATA DETERMINED BY AUTHOR: K.ISHIKAWA,E.SUZUKI,M.TANOKURA,K.TAKAHASHI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanyl-specific ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5615
Polymers11,1521
Non-polymers4094
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.690, 88.690, 88.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-991-

UNX

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Components

#1: Protein Guanyl-specific ribonuclease T1 / RNase T1


Mass: 11151.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus oryzae (mold) / Strain: ATCC 42149 / RIB 40 / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1DET.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: BUSTER / Version: 2.13.0 / Classification: refinement
RefinementMethod to determine structure: RE-REFINEMENT
Starting model: PDB ENTRY 1DET

1det


Resolution: 1.95→13.44 Å / Cor.coef. Fo:Fc: 0.9678 / Cor.coef. Fo:Fc free: 0.9672 / SU R Cruickshank DPI: 0.169 / Cross valid method: IN RE-REFINEMENT / σ(F): 0 / Stereochemistry target values: Engh and Huber EH99
RfactorNum. reflection% reflectionSelection details
Rfree0.1649 416 4.97 %RANDOM
Rwork0.1384 ---
obs0.1398 8365 97.27 %-
Displacement parametersBiso mean: 37.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.95→13.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 27 46 853
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011518HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.12687HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d313SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes264HARMONIC5
X-RAY DIFFRACTIONt_it1518HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.39
X-RAY DIFFRACTIONt_other_torsion13.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion103SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1609SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.18 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.1808 109 4.74 %
Rwork0.138 2189 -
all0.14 2298 -
obs--97.27 %
Refinement TLS params.Method: refined / Origin x: 25.1322 Å / Origin y: -46.7198 Å / Origin z: 14.8879 Å
111213212223313233
T-0.0472 Å20.0187 Å20.0227 Å2--0.0453 Å2-0.0343 Å2---0.0664 Å2
L4.4966 °2-0.4423 °2-1.0064 °2-1.6031 °2-0.2293 °2--2.3279 °2
S0.0165 Å °-0.3042 Å °-0.1118 Å °0.3166 Å °-0.001 Å °-0.0561 Å °-0.091 Å °0.2916 Å °-0.0155 Å °
Refinement TLS groupSelection details: { A|* }

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