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- PDB-5bu4: RIBONUCLEASE T1 COMPLEX WITH 2'GMP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5bu4
TitleRIBONUCLEASE T1 COMPLEX WITH 2'GMP
ComponentsPROTEIN (RIBONUCLEASE T1)
KeywordsHYDROLASE / HYDROLASE(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 / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLoris, R. / Devos, S. / Langhorst, U. / Decanniere, K. / Bouckaert, J. / Maes, D. / Transue, T.R. / Steyaert, J.
CitationJournal: Proteins / Year: 1999
Title: Conserved water molecules in a large family of microbial ribonucleases.
Authors: Loris, R. / Langhorst, U. / De Vos, S. / Decanniere, K. / Bouckaert, J. / Maes, D. / Transue, T.R. / Steyaert, J.
History
DepositionSep 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 20, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4983
Polymers11,0951
Non-polymers4032
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.470, 48.100, 50.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (RIBONUCLEASE T1)


Mass: 11094.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Plasmid: PMC5-RT1 / Gene (production host): SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.26 Å3/Da / Density % sol: 46 %
Crystal growpH: 4.2 / Details: 20 MM NA-ACETATE PH 4.2 2 MM CACL2 55 % MPD
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Zegers, I., (1998) Nat. Struct. Biol., 5, 280.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
22 mM2'GMP1drop
320 mM1dropNaOAc
42 mM1dropCaCl2
555 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→20 Å / Num. obs: 9833 / % possible obs: 93.8 % / Redundancy: 38.7 % / Rsym value: 0.188 / Net I/σ(I): 23.64
Reflection
*PLUS
Num. measured all: 380597 / Rmerge(I) obs: 0.188
Reflection shell
*PLUS
Rmerge(I) obs: 0.978

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RESTRAINrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7GSP

7gsp


Resolution: 1.77→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 850 9.8 %RANDOM R VALUE (WORKING + TEST SET) : NULL
Rwork0.172 ---
obs-9521 93.8 %-
Refinement stepCycle: LAST / Resolution: 1.77→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 25 94 903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.354
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.013

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