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- PDB-5rnt: X-RAY ANALYSIS OF CUBIC CRYSTALS OF THE COMPLEX FORMED BETWEEN RI... -

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Basic information

Entry
Database: PDB / ID: 5rnt
TitleX-RAY ANALYSIS OF CUBIC CRYSTALS OF THE COMPLEX FORMED BETWEEN RIBONUCLEASE T1 AND GUANOSINE-3',5'-BISPHOSPHATE
ComponentsRIBONUCLEASE 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-3',5'-DIPHOSPHATE / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsSaenger, W. / Heinemann, U. / Lenz, A.
CitationJournal: Acta Crystallogr.,Sect.B / Year: 1991
Title: X-ray analysis of cubic crystals of the complex formed between ribonuclease T1 and guanosine-3',5'-bisphosphate.
Authors: Lenz, A. / Heinemann, U. / Maslowska, M. / Saenger, W.
History
DepositionMar 28, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5382
Polymers11,0951
Non-polymers4431
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Atom site foot note1: RESIDUES PRO 39 AND PRO 55 ARE CIS PROLINES.
Components on special symmetry positions
IDModelComponents
11A-200-

HOH

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Components

#1: 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) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-PGP / GUANOSINE-3',5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 49.32 %
Crystal grow
*PLUS
pH: 4.5 / Method: microdialysis
Details: enzyme was dissoloved sodium acetate buffer, containing protein and calcium acetate.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %lyophilized enzyme1buttom
210 mMsodium acetate1buttom
30.025 %protein1buttom
42 mMcalcium acetate1buttom
540 %MPD1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 3.2 Å / Num. obs: 1408 / Observed criterion σ(I): 1 / Num. measured all: 4274 / Rmerge(I) obs: 0.043

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 3.2→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.166 1540
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms781 0 28 83 892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0540.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0050.015
X-RAY DIFFRACTIONp_chiral_restr0.1440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1290.15
X-RAY DIFFRACTIONp_multtor_nbd0.1340.15
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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