SAXSdb — 1efr

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1. Structure Basics

entry_id	1efr
deposition_date	1996-05-24
title	BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH THE PEPTIDE ANTIBIOTIC EFRAPEPTIN
keywords	;ANTIBIOTIC, ATP PHOSPHORYLASE, HYDROGEN ION TRANSPORT, ATP SYNTHASE, F1-ATPASE, IONOPHORE, HYDROLASE-ANTIBIOTIC COMPLEX, EFRAPEPTIN, F1-ATPASE-ANTIBIOTIC COMPLEX ;; HYDROLASE/ANTIBIOTIC
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	41.77 Å
rg_electron	40.93 Å
i0	1536330000.00
molecular_weight	327310.0 kDa
excluded_volume	411490 Å³
envelope_volume	517010 Å³
shell_volume	96924 Å³
envelope_diameter	133.4 Å
shell_rg	51.98 Å
envelope_rg	40.51 Å
shape_rg	40.94 Å
total_rg	41.34 Å
total_atoms	22992
n_residues	2991
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	125.3 Å
rg_real	41.47 Å
rg_real_error	0.57 Å
i0_real	1.5360e+09
i0_real_error	2.4980e+07
rg_reciprocal	41.77 Å
i0_reciprocal	1537000000.0000
total_estimate	0.8955
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	56.1 Å
skewness	0.020
kurtosis	-0.563
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	388600000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.926

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT ALPHA
formula_weight	55302.2 kDa
ec_number	3.6.1.34
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	23527

EKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA

Entity 2 polymer

description	BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT BETA
formula_weight	51757.8 kDa
ec_number	3.6.1.34
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

AAQASPSPKAGATTGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIRIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS

Entity 3 polymer

description	BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT GAMMA
formula_weight	30185.7 kDa
ec_number	3.6.1.34
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEKADIKTPEDKKKHLIIGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFSLDTISSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAAL

Entity 4 polymer

description	EFRAPEPTIN C
formula_weight	1592.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q

XXAXAALXGAAXAGLAX

Source

organism	TOLYPOCLADIUM INFLATUM
ncbi_taxonomy_id	29910

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

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

Entity 7 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	535

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6. Citations (5)

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length_a	285.700 Å
length_b	107.400 Å
length_c	139.500 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.100 Å
resolution_low	5.500 Å
r_factor	—
r_work	0.1770
r_free	0.2200

fit	/app/data/saxs_computation/ef/1efr/1efr.fit
pddf	/app/data/pr_computation/ef/1efr/1efr.pr.out
profile	/app/data/saxs_computation/ef/1efr/1efr.dat

BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH THE PEPTIDE ANTIBIOTIC EFRAPEPTIN

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

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (5)

7. Files & Curves (10)

Files (7)

Curves (3)