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1b2m

;THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS. ;

Method: X-RAY DIFFRACTION D_max: 63.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1b2m
deposition_date	1998-11-27
title	;THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS. ;
keywords	HYDROLASE, ENDORIBONUCLEASE, HYDROLASE/RNA, HYDROLASE-RNA complex; HYDROLASE/RNA
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	19.57 Å
rg_electron	18.79 Å
i0	12948600.00
molecular_weight	23917.0 kDa
excluded_volume	28438 Å³
envelope_volume	34176 Å³
shell_volume	15839 Å³
envelope_diameter	64.4 Å
shell_rg	23.99 Å
envelope_rg	18.91 Å
shape_rg	18.71 Å
total_rg	19.72 Å
total_atoms	1682
n_residues	211
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	63.4 Å
rg_real	19.60 Å
rg_real_error	0.42 Å
i0_real	1.2950e+07
i0_real_error	1.5390e+05
rg_reciprocal	19.59 Å
i0_reciprocal	12950000.0000
total_estimate	0.6463
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.3 Å
skewness	0.381
kurtosis	-0.377
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	2578000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 0.999; Sysdev: 0.278; Positv: 1.000; Valcen: 0.964; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (7)

;Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis. ;

Biochemistry (1999)

PMID: 10029539 · DOI: 10.1021/bi982612q PRIMARY

;Three-Dimensional Structure of Gln 25-Ribonuclease T1 at 1.84 Angstroms Resolution: Structural Variations at the Base Recognition and Catalytic Sites ;

Biochemistry (1992)

;Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding ;

Biochemistry (1989)

;Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution ;

J.Biol.Chem. (1988)

;Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution ;

Acta Crystallogr.,Sect.B (1987)

Structure and Function of the Enzyme Ribonuclease T1

Fresenius Z.Anal.Chem. (1987)

Crystallization of Ribonuclease T1

J.Mol.Biol. (1980)

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length_a	69.910 Å
length_b	90.290 Å
length_c	33.980 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.000 Å
resolution_low	8.000 Å
r_factor	0.1870
r_work	0.1870
r_free	0.2540

description	5'-R(GP(U34))-3'
formula_weight	620.4 kDa
src_method	syn
entity_count	3

type	polyribonucleotide
strand_id	C,D,E
atom_count	1774

;THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS. ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 water

6. Citations (7)

7. Files & Curves (10)

Files (7)

Curves (3)

description	RIBONUCLEASE T1
formula_weight	11093.6 kDa
ec_number	3.1.27.3
mutation	GLN 25 VARIANT
src_method	nat
entity_count	2

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	92

fit	/app/data/saxs_computation/b2/1b2m/1b2m.fit
pddf	/app/data/pr_computation/b2/1b2m/1b2m.pr.out
profile	/app/data/saxs_computation/b2/1b2m/1b2m.dat

type	polypeptide(L)
strand_id	A,B