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1d2h

CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLHOMOCYSTEINE

Method: X-RAY DIFFRACTION D_max: 108.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d2h
deposition_date	1999-10-11
title	CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLHOMOCYSTEINE
keywords	METHYLTRANSFERASE, 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	37.32 Å
rg_electron	36.58 Å
i0	196715000.00
molecular_weight	113400.0 kDa
excluded_volume	141970 Å³
envelope_volume	196160 Å³
shell_volume	44688 Å³
envelope_diameter	108.0 Å
shell_rg	43.66 Å
envelope_rg	34.53 Å
shape_rg	36.59 Å
total_rg	37.04 Å
total_atoms	7984
n_residues	1008
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	108.2 Å
rg_real	37.09 Å
rg_real_error	0.63 Å
i0_real	1.9670e+08
i0_real_error	2.7740e+06
rg_reciprocal	37.23 Å
i0_reciprocal	196700000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	54.1 Å
skewness	-0.021
kurtosis	-0.734
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	25280000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.488

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	GLYCINE N-METHYLTRANSFERASE
formula_weight	32432.8 kDa
ec_number	2.1.1.20
mutation	R175K
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8492

VDSVYRTRSLGVAAEGIPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHKNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKKTG

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 2 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	508

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6. Citations (1)

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length_a	77.900 Å
length_b	77.900 Å
length_c	227.100 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43
int_tables_number	78
crystal_system	—

resolution	3.000 Å
resolution_low	10.000 Å
r_factor	0.1950
r_work	0.1950
r_free	0.2470

fit	/app/data/saxs_computation/d2/1d2h/1d2h.fit
pddf	/app/data/pr_computation/d2/1d2h/1d2h.pr.out
profile	/app/data/saxs_computation/d2/1d2h/1d2h.dat

CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLHOMOCYSTEINE

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