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1dfo

;CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE ;

Method: X-RAY DIFFRACTION D_max: 121.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dfo
deposition_date	1999-11-20
title	;CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE ;
keywords	ALPHA PLP ASPARTATE, AMINO TRANSFERASE, (AAT)-LIKE FOLD, TRANSFERASE; TRANSFERASE
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	37.28 Å
rg_electron	36.74 Å
i0	503583000.00
molecular_weight	181980.0 kDa
excluded_volume	227040 Å³
envelope_volume	267310 Å³
shell_volume	58803 Å³
envelope_diameter	132.7 Å
shell_rg	44.35 Å
envelope_rg	36.54 Å
shape_rg	36.70 Å
total_rg	37.27 Å
total_atoms	12816
n_residues	1666
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	121.2 Å
rg_real	37.20 Å
rg_real_error	0.84 Å
i0_real	5.0360e+08
i0_real_error	9.1730e+06
rg_reciprocal	37.25 Å
i0_reciprocal	503600000.0000
total_estimate	0.8937
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.3 Å
skewness	0.259
kurtosis	-0.456
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	346400000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.895

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	SERINE HYDROXYMETHYLTRANSFERASE
formula_weight	45372.5 kDa
ec_number	2.1.2.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13204

MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLEPGDTVLGMNLAHGGHLTHGSPVNFSGKLYNIVPYGIDATGHIDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVEVFLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIERIKGKVLDICARYPVYA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
formula_weight	306.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
formula_weight	473.4 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	388

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6. Citations (1)

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length_a	77.460 Å
length_b	172.240 Å
length_c	95.050 Å
angle_alpha	90.00 °
angle_beta	104.12 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.400 Å
resolution_low	20.000 Å
r_factor	0.1740
r_work	0.1740
r_free	0.1960

fit	/app/data/saxs_computation/df/1dfo/1dfo.fit
pddf	/app/data/pr_computation/df/1dfo/1dfo.pr.out
profile	/app/data/saxs_computation/df/1dfo/1dfo.dat

;CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE ;

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