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1d4f

CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE

Method: X-RAY DIFFRACTION D_max: 112.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d4f
deposition_date	2000-06-22
title	CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE
keywords	S-adenosylhomocysteine hydrolase, AdoHcyase, AdoHcy, Mutagenesis, X-ray crystal structure, Enzyme structure, HYDROLASE; HYDROLASE
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	34.88 Å
rg_electron	34.42 Å
i0	565107000.00
molecular_weight	193090.0 kDa
excluded_volume	241630 Å³
envelope_volume	278640 Å³
shell_volume	63729 Å³
envelope_diameter	124.5 Å
shell_rg	43.46 Å
envelope_rg	34.60 Å
shape_rg	34.46 Å
total_rg	34.86 Å
total_atoms	13532
n_residues	1720
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	112.5 Å
rg_real	34.71 Å
rg_real_error	0.67 Å
i0_real	5.6510e+08
i0_real_error	9.5980e+06
rg_reciprocal	34.82 Å
i0_reciprocal	565200000.0000
total_estimate	0.8867
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.0 Å
skewness	0.198
kurtosis	-0.385
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	375500000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.953

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	S-ADENOSYLHOMOCYSTEINE HYDROLASE
formula_weight	47479.7 kDa
ec_number	3.3.1.1
mutation	D244E
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14005

ADKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREMYSASKPLKGARIAGCLHMTVETAVLIETLVALGAEVRWSSCNIFSTQDHAAAAIAKAGIPVFAWKGETDEEYLWCIEQTLHFKDGPLNMILDDGGDLTNLIHTKHPQLLSGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIEPINALQAAMEGYEVTTMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYLLKNGHRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMPINGPFKPDHYRY

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	ADENOSINE
formula_weight	267.2 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	473

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6. Citations (1)

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length_a	91.000 Å
length_b	223.000 Å
length_c	91.230 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.800 Å
resolution_low	8.000 Å
r_factor	0.1970
r_work	0.1970
r_free	0.2480

fit	/app/data/saxs_computation/d4/1d4f/1d4f.fit
pddf	/app/data/pr_computation/d4/1d4f/1d4f.pr.out
profile	/app/data/saxs_computation/d4/1d4f/1d4f.dat

CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE

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