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9v4h

Prenyltransferase Ord1 Q216A-FSPP

Method: X-RAY DIFFRACTION D_max: 119.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v4h
deposition_date	2025-05-23
title	Prenyltransferase Ord1 Q216A-FSPP
keywords	Transferase, Prenyltransferase; 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	34.98 Å
rg_electron	34.35 Å
i0	232178000.00
molecular_weight	119900.0 kDa
excluded_volume	149220 Å³
envelope_volume	199980 Å³
shell_volume	48495 Å³
envelope_diameter	121.0 Å
shell_rg	40.84 Å
envelope_rg	34.15 Å
shape_rg	34.38 Å
total_rg	34.69 Å
total_atoms	8397
n_residues	1121
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	119.6 Å
rg_real	34.95 Å
rg_real_error	0.94 Å
i0_real	2.3220e+08
i0_real_error	3.4670e+06
rg_reciprocal	34.97 Å
i0_reciprocal	232200000.0000
total_estimate	0.8748
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	42.5 Å
skewness	0.353
kurtosis	-0.217
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	31360000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.964

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	prenyltransferase
formula_weight	36138.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8450

MTDIDVPQVADPEVAAMVRAEVEGRWPLGVSGLDEVVRYGLVPFGKMMGPWLLIRSALAVGGDIATALPAAVALECVQVGAMMHDDIIDCDAQRRSKPAAHTVFGEPTAIVGGDGLFFHGFAALSECREAGAPAERVAQAFTVLSRAGLRIGSAALREIRMSREICSVQDYLDMIADKSGALLWMACGVGGTLGGADEAALKALSQYSDQLGIAYAIRDDLMAYDGTRAGKPNISDVRNGRPTLPVLLAHERAPREQQLRIERLLADTAAPAAERYKAMADLVGAYDGAQAAREVSHRHVQLATRALQTLPPSPHRDALEDLTVPGRLVLEHHHHHH

Source

organism	Streptomyces sp. KS84
ncbi_taxonomy_id	746563
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE
formula_weight	398.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	53

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6. Citations (1)

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length_a	58.930 Å
length_b	71.870 Å
length_c	84.000 Å
angle_alpha	86.28 °
angle_beta	69.39 °
angle_gamma	89.99 °
z_pdb	4

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.200 Å
resolution_low	44.260 Å
r_factor	0.2379
r_work	0.2357
r_free	0.2534

fit	/app/data/saxs_computation/v4/9v4h/9v4h.fit
pddf	/app/data/pr_computation/v4/9v4h/9v4h.pr.out
profile	/app/data/saxs_computation/v4/9v4h/9v4h.dat

Prenyltransferase Ord1 Q216A-FSPP

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