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9wxs

Silver-bound E.coli Malate dehydrogenase (C251S)

Method: X-RAY DIFFRACTION D_max: 103.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wxs
deposition_date	2025-09-25
title	Silver-bound E.coli Malate dehydrogenase (C251S)
keywords	Dehydrogenase, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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	33.73 Å
rg_electron	32.95 Å
i0	227900000.00
molecular_weight	124510.0 kDa
excluded_volume	157640 Å³
envelope_volume	197900 Å³
shell_volume	49073 Å³
envelope_diameter	109.4 Å
shell_rg	40.85 Å
envelope_rg	32.16 Å
shape_rg	32.98 Å
total_rg	33.47 Å
total_atoms	8734
n_residues	1205
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	103.4 Å
rg_real	33.57 Å
rg_real_error	0.75 Å
i0_real	2.2790e+08
i0_real_error	3.4940e+06
rg_reciprocal	33.67 Å
i0_reciprocal	227900000.0000
total_estimate	0.9040
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	48.4 Å
skewness	0.103
kurtosis	-0.541
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	48140000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.932

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Malate dehydrogenase
formula_weight	32352.1 kDa
ec_number	1.1.1.37
mutation	C251S
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	9327

MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVESAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SILVER ION
formula_weight	107.9 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	593

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6. Citations (1)

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length_a	51.560 Å
length_b	156.280 Å
length_c	77.390 Å
angle_alpha	90.00 °
angle_beta	109.20 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.560 Å
resolution_low	36.543 Å
r_factor	0.2675
r_work	0.2660
r_free	0.2965

fit	/app/data/saxs_computation/wx/9wxs/9wxs.fit
pddf	/app/data/pr_computation/wx/9wxs/9wxs.pr.out
profile	/app/data/saxs_computation/wx/9wxs/9wxs.dat

Silver-bound E.coli Malate dehydrogenase (C251S)

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