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- PDB-3urp: Re-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-... -

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Basic information

Entry
Database: PDB / ID: 3urp
TitleRe-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-3',5'-diphosphate and phosphate ion bound
ComponentsGuanyl-specific ribonuclease T1
KeywordsHYDROLASE / ROLL / ENDORIBONUCLEASE / RNA
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-3',5'-DIPHOSPHATE / PHOSPHATE ION / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsSmart, O.S. / Womack, T.O. / Flensburg, C. / Keller, P. / Sharff, A. / Paciorek, W. / Vonrhein, C. / Bricogne, G.
CitationJournal: Eur.J.Biochem. / Year: 1993
Title: Three-dimensional structure of the ternary complex between ribonuclease T1, guanosine 3 ,5 -bisphosphate and inorganic phosphate at 0.19 nm resolution
Authors: Lenz, A. / Choe, H.W. / Granzin, J. / Heinemann, U. / Saenger, W.
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 3URP REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R5RNTSF ...THIS ENTRY 3URP REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R5RNTSF DETERMINED BY THE AUTHORS OF THE PDB ENTRY 5RNT: W.SAENGER,U.HEINEMANN,A.LENZ

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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)11,6334
Polymers11,0951
Non-polymers5383
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.470, 86.470, 86.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 11094.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-PGP / GUANOSINE-3',5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.43 Å3/Da / Density % sol: 49.34 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5RNT.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.13.0refinement
PDB_EXTRACT3.11data extraction
MOLREPphasing
BUSTER2.13.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SYU

3syu


Resolution: 3.19→43.24 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber EH99
Details: 1. X-RAY WEIGHT 8.00. 2. HYDROPHOBIC VOID CORRECTION ON. 3. PGP RESTRAINTS FROM GRADE 1.1.1 USING MOGUL AND RM1 QM. 4. SIMILARITY, NCS REPRESENTATION: NONE, TARGET RESTRAINTS: LSSR WEIGHT 1. ...Details: 1. X-RAY WEIGHT 8.00. 2. HYDROPHOBIC VOID CORRECTION ON. 3. PGP RESTRAINTS FROM GRADE 1.1.1 USING MOGUL AND RM1 QM. 4. SIMILARITY, NCS REPRESENTATION: NONE, TARGET RESTRAINTS: LSSR WEIGHT 1.5 TARGET STRUCTURE 3SYU.PDB.
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 102 5.44 %RANDOM
Rwork0.2018 ---
obs0.2035 1874 98.89 %-
Displacement parametersBiso max: 79.17 Å2 / Biso mean: 26.6536 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.465 Å
Refinement stepCycle: LAST / Resolution: 3.19→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms776 0 34 8 818
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d261SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes140HARMONIC5
X-RAY DIFFRACTIONt_it846HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion103SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact906SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d846HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg1171HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion16.3
LS refinement shellResolution: 3.19→3.57 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2665 31 5.92 %
Rwork0.2305 493 -
all0.2325 524 -
obs--98.89 %

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