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1dze

Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K

Method: X-RAY DIFFRACTION D_max: 63.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dze
deposition_date	2000-02-25
title	Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K
keywords	;BACTERIORHODOPSIN, PROTON PUMP, MEMBRANE PROTEIN, RETINAL PROTEIN, PHOTORECEPTOR, REACTION INTERMEDIATE, HALOBACTERIA, ION PUMP, HELIX, SLIDING ;; BACTERIORHODOPSIN
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	19.45 Å
rg_electron	18.47 Å
i0	9153600.00
molecular_weight	28195.0 kDa
excluded_volume	37753 Å³
envelope_volume	40660 Å³
shell_volume	18418 Å³
envelope_diameter	62.2 Å
shell_rg	24.66 Å
envelope_rg	18.84 Å
shape_rg	18.41 Å
total_rg	19.76 Å
total_atoms	1986
n_residues	225
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	63.2 Å
rg_real	19.46 Å
rg_real_error	0.34 Å
i0_real	9.1540e+06
i0_real_error	9.9610e+04
rg_reciprocal	19.46 Å
i0_reciprocal	9154000.0000
total_estimate	0.8927
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.4 Å
skewness	0.334
kurtosis	-0.451
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	2025000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	BACTERIORHODOPSIN (M INTERMEDIATE)
formula_weight	26814.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2004

QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSAGDGAAATS

Entity 2 branched

description	beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose
formula_weight	504.4 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	RETINAL
formula_weight	284.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
formula_weight	733.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	2,3-DI-PHYTANYL-GLYCEROL
formula_weight	653.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
formula_weight	885.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
formula_weight	807.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	18

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6. Citations (2)

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length_a	102.400 Å
length_b	102.400 Å
length_c	112.300 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 6 2 2
int_tables_number	177
crystal_system	—

resolution	2.500 Å
resolution_low	8.000 Å
r_factor	0.2570
r_work	0.2570
r_free	0.2830

fit	/app/data/saxs_computation/dz/1dze/1dze.fit
pddf	/app/data/pr_computation/dz/1dze/1dze.pr.out
profile	/app/data/saxs_computation/dz/1dze/1dze.dat