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9pzl

Pyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions

Method: X-RAY DIFFRACTION D_max: 160.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pzl
deposition_date	2025-08-11
last_revision	2025-08-20
title	Pyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions
keywords	PHOSPHOTRANSFERASE, ATP-BINDING, PEP BINDING DIKINASE, 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	52.19 Å
rg_electron	51.91 Å
i0	2248480000.00
molecular_weight	388540.0 kDa
excluded_volume	482650 Å³
envelope_volume	667980 Å³
shell_volume	105160 Å³
envelope_diameter	169.7 Å
shell_rg	57.96 Å
envelope_rg	50.07 Å
shape_rg	51.93 Å
total_rg	52.02 Å
total_atoms	27192
n_residues	3488
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	160.8 Å
rg_real	52.90 Å
rg_real_error	0.51 Å
i0_real	2.2080e+09
i0_real_error	3.6970e+07
rg_reciprocal	52.32 Å
i0_reciprocal	2249000000.0000
total_estimate	0.7032
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	69.7 Å
skewness	0.216
kurtosis	-0.388
angular_range	— – 0.1500 Å⁻¹
current_alpha	1.6850
highest_alpha	109600000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 0.921; Sysdev: 0.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.490

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Pyruvate, phosphate dikinase
formula_weight	96771.3 kDa
ec_number	2.7.9.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	27192

MAKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNNK

Source

organism	Clostridium symbiosum
ncbi_taxonomy_id	1512
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	12

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6. Citations (1)

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length_a	108.695 Å
length_b	118.475 Å
length_c	170.806 Å
angle_alpha	90.00 °
angle_beta	90.40 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	3.000 Å
resolution_low	47.533 Å
r_factor	0.2245
r_work	0.2187
r_free	0.3021

fit	/app/data/saxs_computation/pz/9pzl/9pzl.fit
pddf	/app/data/pr_computation/pz/9pzl/9pzl.pr.out
profile	/app/data/saxs_computation/pz/9pzl/9pzl.dat

Pyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions

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