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- PDB-1q9e: RNase T1 variant with adenine specificity -

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Basic information

Entry
Database: PDB / ID: 1q9e
TitleRNase T1 variant with adenine specificity
ComponentsGuanyl-specific ribonuclease T1 precursor
KeywordsHYDROLASE / Ribonuclease / Adenine specificity
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
Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCzaja, R. / Struhalla, M. / Hoeschler, K. / Saenger, W. / Straeter, N. / Hahn, U.
Citation
Journal: Biochemistry / Year: 2004
Title: RNase T1 Variant RV Cleaves Single-Stranded RNA after Purines Due to Specific Recognition by the Asn46 Side Chain Amide.
Authors: Czaja, R. / Struhalla, M. / Saenger, W. / Hahn, U.
History
DepositionAug 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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: Guanyl-specific ribonuclease T1 precursor
B: Guanyl-specific ribonuclease T1 precursor
C: Guanyl-specific ribonuclease T1 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6345
Polymers33,3893
Non-polymers2442
Water4,936274
1
A: Guanyl-specific ribonuclease T1 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2522
Polymers11,1301
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanyl-specific ribonuclease T1 precursor


Theoretical massNumber of molelcules
Total (without water)11,1301
Polymers11,1301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Guanyl-specific ribonuclease T1 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2522
Polymers11,1301
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.500, 56.500, 158.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 11129.745 Da / Num. of mol.: 3 / Mutation: K41E, Y42F, N43R, Y45W, E46N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: RNTA / Plasmid: pA2T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 279 K / pH: 9
Details: PEG4000, magnesium chloride, Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 279K, pH 9.00
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mMRNase T1 RV1drop
210 mMTris-HCl1droppH8.5
3100 mMTris-HCl1reservoirpH9.0
4200 mM1reservoirMgCl2
520-22 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8459 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 28456 / % possible obs: 90.6 % / Biso Wilson estimate: 21.4 Å2
Reflection shellResolution: 1.7→20 Å / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. obs: 31400 / Num. measured all: 70573 / Rmerge(I) obs: 0.037

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CH0

1ch0


Resolution: 1.7→18.01 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 953216.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1179 4.1 %RANDOM
Rwork0.199 ---
obs0.199 28456 90.5 %-
all-31400 --
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 50.16 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 26.52 Å2
Baniso -1Baniso -2Baniso -3
1-3.22 Å23.78 Å20 Å2
2--3.22 Å20 Å2
3----6.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→18.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 16 274 2688
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.581.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it3.022
X-RAY DIFFRACTIONc_scangle_it4.222.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 19 0.4 %
Rwork0.283 4479 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TMN_XPLOR_PAR.TXTTMN_XPLOR_TOP.TXT
X-RAY DIFFRACTION4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.96
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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