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- PDB-1rn1: THREE-DIMENSIONAL STRUCTURE OF GLN 25-RIBONUCLEASE T1 AT 1.84 ANG... -

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Entry
Database: PDB / ID: 1rn1
TitleTHREE-DIMENSIONAL STRUCTURE OF GLN 25-RIBONUCLEASE T1 AT 1.84 ANGSTROMS RESOLUTION: STRUCTURAL VARIATIONS AT THE BASE RECOGNITION AND CATALYTIC SITES
ComponentsRIBONUCLEASE T1 ISOZYME
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
Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.84 Å
AuthorsArni, R.K. / Pal, G.P. / Ravichandran, K.G. / Tulinsky, A. / Walz Junior, F.G. / Metcalf, P.
Citation
Journal: Biochemistry / Year: 1992
Title: Three-dimensional structure of Gln25-ribonuclease T1 at 1.84-A resolution: structural variations at the base recognition and catalytic sites.
Authors: Arni, R.K. / Pal, G.P. / Ravichandran, K.G. / Tulinsky, A. / Walz Jr., F.G. / Metcalf, P.
#1: Journal: Biochemistry / Year: 1989
Title: Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding
Authors: Kostrewa, D. / Choe, H.-W. / Heinemann, U. / Saenger, W.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, V. / Maslowska, M. / Tokuoka, R. / Saenger, W.
#4: Journal: Fresenius Z.Anal.Chem. / Year: 1987
Title: Structure and Function of the Enzyme Ribonuclease T1
Authors: Arni, R. / Heinemann, U. / Saenger, W.
#5: Journal: J.Mol.Biol. / Year: 1980
Title: Crystallization of Ribonuclease T1
Authors: Martin, P.O. / Tulinsky, A. / Walz, F.G.
History
DepositionNov 22, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE T1 ISOZYME
B: RIBONUCLEASE T1 ISOZYME
C: RIBONUCLEASE T1 ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5696
Polymers33,2813
Non-polymers2883
Water3,225179
1
C: RIBONUCLEASE T1 ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1902
Polymers11,0941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RIBONUCLEASE T1 ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1902
Polymers11,0941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: RIBONUCLEASE T1 ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1902
Polymers11,0941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.710, 37.540, 77.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 39 AND PRO 55 OF ALL CHAINS ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0701, 0.9676, -0.2427), (-0.5247, 0.1711, 0.8339), (0.8484, 0.1858, 0.4957)51.299, 4.649, -14.759
2given(0.5413, 0.6404, 0.5469), (0.0409, 0.6272, -0.7778), (-0.8398, 0.4433, 0.3133)-16.614, 43.666, 67.113
DetailsTHERE ARE THREE MOLECULES IN THE ASYMMETRIC UNIT, REFERRED TO AS CHAINS A, B, AND C. THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *C*.

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Components

#1: Protein RIBONUCLEASE T1 ISOZYME


Mass: 11093.644 Da / Num. of mol.: 3
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHERE ARE THREE SULFATE IONS AT THE CATALYTIC SITES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion / Details: micro seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
155 %1reservoir(NH4)2SO4
20.1 Mpotasssium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.84 Å / Num. all: 24053 / Num. obs: 18062 / % possible obs: 75.1 % / Num. measured all: 53463 / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.84→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.144 -
obs0.144 16957
Refinement stepCycle: LAST / Resolution: 1.84→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 15 179 2495
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it22
X-RAY DIFFRACTIONx_mcangle_it2.92
X-RAY DIFFRACTIONx_scbond_it54.5
X-RAY DIFFRACTIONx_scangle_it6.46
Refinement
*PLUS
Rfactor obs: 0.144
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.030.039
X-RAY DIFFRACTIONx_planar_d0.060.057
X-RAY DIFFRACTIONx_plane_restr0.020.018
X-RAY DIFFRACTIONx_chiral_restr0.150.182

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