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1dxr

Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant (terbutryn complex)

Method: X-RAY DIFFRACTION D_max: 126.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dxr
deposition_date	2000-01-15
title	Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant (terbutryn complex)
keywords	PHOTOSYNTHESIS, SECONDARY QUINONE (QB), TRIAZINE INHIBITOR; PHOTOSYNTHESIS
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	36.87 Å
rg_electron	35.91 Å
i0	260118000.00
molecular_weight	143140.0 kDa
excluded_volume	183790 Å³
envelope_volume	213240 Å³
shell_volume	50044 Å³
envelope_diameter	135.1 Å
shell_rg	41.56 Å
envelope_rg	36.45 Å
shape_rg	35.84 Å
total_rg	36.55 Å
total_atoms	10140
n_residues	1185
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	126.4 Å
rg_real	37.13 Å
rg_real_error	1.21 Å
i0_real	2.6010e+08
i0_real_error	4.8050e+06
rg_reciprocal	36.97 Å
i0_reciprocal	260100000.0000
total_estimate	0.8388
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.2 Å
skewness	0.538
kurtosis	-0.144
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	45610000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.857; Smooth: 0.640

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4. Crystallography & Experiment

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5. Entities & Polymer Info (14)

Entity 1 polymer

description	PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
formula_weight	37450.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	10777

CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Entity 2 polymer

description	PHOTOSYNTHETIC REACTION CENTER H SUBUNIT
formula_weight	28557.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL

Entity 3 polymer

description	PHOTOSYNTHETIC REACTION CENTER L SUBUNIT
formula_weight	30478.1 kDa
mutation	H168F
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWFYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Source

organism	RHODOPSEUDOMONAS VIRIDIS
ncbi_taxonomy_id	1079
host_organism	RHODOPSEUDOMONAS VIRIDIS

Entity 4 polymer

description	PHOTOSYNTHETIC REACTION CENTER M SUBUNIT
formula_weight	35932.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK

Entity 5 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	LAURYL DIMETHYLAMINE-N-OXIDE
formula_weight	229.4 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	BACTERIOCHLOROPHYLL B
formula_weight	909.5 kDa
src_method	syn
entity_count	4

Entity 9 non-polymer

description	BACTERIOPHEOPHYTIN B
formula_weight	887.2 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	MENAQUINONE-9
formula_weight	785.2 kDa
src_method	syn
entity_count	1

Entity 12 non-polymer

description	2-T-BUTYLAMINO-4-ETHYLAMINO-6-METHYLTHIO-S-TRIAZINE
formula_weight	241.4 kDa
src_method	syn
entity_count	1

Entity 13 non-polymer

description	15-cis-1,2-dihydroneurosporene
formula_weight	540.9 kDa
src_method	syn
entity_count	1

Entity 14 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	585

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6. Citations (9)

;Structural basis of the drastically increased initial electron transfer rate in the reaction center from a Rhodopseudomonas viridis mutant described at 2.00-A resolution. ;

J. Biol. Chem. (2000)

PMID: 11005826 · DOI: 10.1074/jbc.M008225200 PRIMARY

;Refined Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to a New Model of the Bound Carotenoid ;

J.Mol.Biol. (1999)

PMID: 10024457 · DOI: 10.1006/JMBI.1998.2532

;Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications ;

Biochim.Biophys.Acta (1998)

;The Coupling of Light-Induced Electron Transfer and Proton Uptake as Derived from Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis Modified at the Binding Site of the Secondary Quinone, Qb ;

Structure (1997)

PMID: 9351808 · DOI: 10.1016/S0969-2126(97)00285-2

;Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis ;

J.Mol.Biol. (1995)

PMID: 7877166 · DOI: 10.1006/JMBI.1994.0097

The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis

Science (1989)

PMID: 17776797 · DOI: 10.1126/SCIENCE.245.4925.1463

Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution

Nature (1985)

PMID: 22439175

;X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis ;

J.Mol.Biol. (1984)

PMID: 6392571 · DOI: 10.1016/S0022-2836(84)80011-X

Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis

J.Mol.Biol. (1982)

PMID: 7131557 · DOI: 10.1016/0022-2836(82)90216-9

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length_a	223.500 Å
length_b	223.500 Å
length_c	113.600 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.000 Å
resolution_low	10.000 Å
r_factor	0.1940
r_work	0.1940
r_free	0.2180

fit	/app/data/saxs_computation/dx/1dxr/1dxr.fit
pddf	/app/data/pr_computation/dx/1dxr/1dxr.pr.out
profile	/app/data/saxs_computation/dx/1dxr/1dxr.dat

Photosynthetic reaction center from Rhodopseudomonas viridis - His L168 Phe mutant (terbutryn complex)

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 (14)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 water

6. Citations (9)

7. Files & Curves (10)

Files (7)

Curves (3)