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11yo

Single-conformation model re-refinement of 2F/S3-rich PSII intermediate structure at 2.09 Angstrom resolution

Method: X-RAY DIFFRACTION D_max: 196.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11yo
deposition_date	2026-03-18
last_revision	2026-04-01
title	Single-conformation model re-refinement of 2F/S3-rich PSII intermediate structure at 2.09 Angstrom resolution
keywords	Model bias Model anti-bias single-conformation model refinement CaMn4O5 composition, PHOTOSYNTHESIS; 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	57.75 Å
rg_electron	57.09 Å
i0	4662220000.00
molecular_weight	707400.0 kDa
excluded_volume	935070 Å³
envelope_volume	1092400 Å³
shell_volume	149990 Å³
envelope_diameter	209.7 Å
shell_rg	64.76 Å
envelope_rg	57.35 Å
shape_rg	57.08 Å
total_rg	57.34 Å
total_atoms	50202
n_residues	5302
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	196.3 Å
rg_real	57.67 Å
rg_real_error	1.52 Å
i0_real	4.6620e+09
i0_real_error	8.8920e+07
rg_reciprocal	57.80 Å
i0_reciprocal	4663000000.0000
total_estimate	0.8651
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.4 Å
skewness	0.329
kurtosis	-0.337
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0003
highest_alpha	643100000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.805

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4. Crystallography & Experiment

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5. Entities & Polymer Info (35)

Entity 1 polymer

description	Photosystem II protein D1 1
formula_weight	38265.6 kDa
ec_number	1.10.3.9
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,a
atom_count	52261

MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLA

Entity 2 polymer

description	Photosystem II CP47 reaction center protein
formula_weight	56656.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,b

MGLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSSIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSGIDPELSPEQVEWGFYQKVGDVTTRRKEAV

Entity 3 polymer

description	Photosystem II CP43 reaction center protein
formula_weight	50287.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,c

MVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD

Entity 4 polymer

description	Photosystem II D2 protein
formula_weight	39388.2 kDa
ec_number	1.10.3.9
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,d

MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL

Entity 5 polymer

description	Cytochrome b559 subunit alpha
formula_weight	9580.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,e

MAGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFLEQLK

Entity 6 polymer

description	Cytochrome b559 subunit beta
formula_weight	5067.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,f

MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR

Entity 7 polymer

description	Photosystem II reaction center protein H
formula_weight	7358.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,h

MARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVSWKALG

Entity 8 polymer

description	Photosystem II reaction center protein I
formula_weight	4438.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,i

METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE

Entity 9 polymer

description	Photosystem II reaction center protein J
formula_weight	4105.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,j

MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL

Entity 10 polymer

description	Photosystem II reaction center protein K
formula_weight	5028.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,k

MIDALVLVAKLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR

Entity 11 polymer

description	Photosystem II reaction center protein L
formula_weight	4299.0 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,l

MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN

Entity 12 polymer

description	Photosystem II reaction center protein M
formula_weight	4009.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,m

MEVNQLGLIATALFVLVPSVFLIILYVQTESQQKSS

Entity 13 polymer

description	Photosystem II manganese-stabilizing polypeptide
formula_weight	29637.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	O,o

MKYRILMATLLAVCLGIFSLSAPAFAAKQTLTYDDIVGTGLANKCPTLDDTARGAYPIDSSQTYRIARLCLQPTTFLVKEEPKNKRQEAEFVPTKLVTRETTSLDQIQGELKVNSDGSLTFVEEDGIDFQPVTVQMAGGERIPLLFTVKNLVASTQPNVTSITTSTDFKGEFNVPSYRTANFLDPKGRGLASGYDSAIALPQAKEEELARANVKRFSLTKGQISLNVAKVDGRTGEIAGTFESEQLSDDDMGAHEPHEVKIQGVFYASIEPA

Entity 14 polymer

description	Photosystem II protein Y
formula_weight	4590.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	R,r

MDWRVLVVLLPVLLAAGWAVRNILPYAVKQVQKLLQKAKAA

Entity 15 polymer

description	Photosystem II reaction center protein T
formula_weight	3906.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	T,t

METITYVFIFACIIALFFFAIFFREPPRITKK

Entity 16 polymer

description	Photosystem II 12 kDa extrinsic protein
formula_weight	15031.0 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	U,u

MQRLGRWLALAYFVGVSLLGWINWSAPTLAATASTEEELVNVVDEKLGTAYGEKIDLNNTNIAAFIQYRGLYPTLAKLIVKNAPYESVEDVLNIPGLTERQKQILRENLEHFTVTEVETALVEGGDRYNNGLYK

Entity 17 polymer

description	Cytochrome c-550
formula_weight	18046.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	V,v

MLKKCVWLAVALCLCLWQFTMGTALAAELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADIFPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGKVYY

Entity 18 polymer

description	Photosystem II reaction center X protein
formula_weight	4322.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	X,x

MTITPSLKGFFIGLLSGAVVLGLTFAVLIAISQIDKVQRSL

Entity 19 polymer

description	Photosystem II reaction center protein Ycf12
formula_weight	5039.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Y,y

MGIFNGIIEFLSNINFEVIAQLTMIAMIGIAGPMIIFLLAVRRGNL

Entity 20 polymer

description	Photosystem II reaction center protein Z
formula_weight	6766.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Z,z

MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV

Entity 21 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	2

Entity 22 non-polymer

description	CHLOROPHYLL A
formula_weight	893.5 kDa
src_method	syn
entity_count	70

Entity 23 non-polymer

description	BETA-CAROTENE
formula_weight	536.9 kDa
src_method	syn
entity_count	22

Entity 24 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 25 non-polymer

description	;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ;
formula_weight	749.2 kDa
src_method	syn
entity_count	4

Entity 26 non-polymer

description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
formula_weight	795.1 kDa
src_method	syn
entity_count	8

Entity 27 non-polymer

description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
formula_weight	949.3 kDa
src_method	syn
entity_count	9

Entity 28 non-polymer

description	STEARIC ACID
formula_weight	284.5 kDa
src_method	syn
entity_count	38

Entity 29 non-polymer

description	CA-MN4-O5 CLUSTER
formula_weight	339.8 kDa
src_method	syn
entity_count	2

Entity 30 non-polymer

description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
formula_weight	787.2 kDa
src_method	syn
entity_count	13

Entity 31 non-polymer

description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
formula_weight	723.0 kDa
src_method	syn
entity_count	10

Entity 32 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	2

Entity 33 non-polymer

description	PHEOPHYTIN A
formula_weight	871.2 kDa
src_method	syn
entity_count	4

Entity 34 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	4

Entity 35 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1994

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6. Citations (1)

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length_a	116.958 Å
length_b	221.646 Å
length_c	307.786 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.090 Å
resolution_low	33.650 Å
r_factor	—
r_work	0.1835
r_free	0.2433

fit	/app/data/saxs_computation/1y/11yo/11yo.fit
pddf	/app/data/pr_computation/1y/11yo/11yo.pr.out
profile	/app/data/saxs_computation/1y/11yo/11yo.dat

Single-conformation model re-refinement of 2F/S3-rich PSII intermediate structure at 2.09 Angstrom resolution

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 (35)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 polymer

Polymer

Entity 17 polymer

Polymer

Entity 18 polymer

Polymer

Entity 19 polymer

Polymer

Entity 20 polymer

Polymer

Entity 21 non-polymer

Entity 22 non-polymer

Entity 23 non-polymer

Entity 24 non-polymer

Entity 25 non-polymer

Entity 26 non-polymer

Entity 27 non-polymer

Entity 28 non-polymer

Entity 29 non-polymer

Entity 30 non-polymer

Entity 31 non-polymer

Entity 32 non-polymer

Entity 33 non-polymer

Entity 34 non-polymer

Entity 35 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)