SAXSdb — 3zpn

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN

THERMOSYNECHOCOCCUS ELONGATUS

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–116 Chain B； UniProt 2–116	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：35% W/V PEG 3350, 300MM POTASSIUM THIOCYANATE	Resolution 2.36 Å R-free 0.234
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–116 Chain D； UniProt 2–116	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：35% W/V PEG 3350, 300MM POTASSIUM THIOCYANATE	Resolution 2.36 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3ZPN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7DXA PSII intermediate Psb28-RC47 Deposited 2021-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–116（116 aa）	Not recorded	SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CLA CHLOROPHYLL A × 22 PHO PHEOPHYTIN A × 2 BCR BETA-CAROTENE × 6 CL CHLORIDE ION × 1 MGE (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 UNL UNKNOWN LIGAND × 2 LMT DODECYL-BETA-D-MALTOSIDE × 3 FE2 FE (II) ION × 1 PQ9 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 HTG heptyl 1-thio-beta-D-glucopyranoside × 1 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
7DXH Cryo-EM structure of PSII intermediate Psb28-PSII complex Deposited 2021-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–116（116 aa）	Not recorded	MGE (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE × 7 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 CLA CHLOROPHYLL A × 34 BCR BETA-CAROTENE × 9 CL CHLORIDE ION × 2 DGD DIGALACTOSYL DIACYL GLYCEROL (DGDG) × 4 PHO PHEOPHYTIN A × 2 LMT DODECYL-BETA-D-MALTOSIDE × 3 FE2 FE (II) ION × 1 PQ9 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE × 1 UNL UNKNOWN LIGAND × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HTG heptyl 1-thio-beta-D-glucopyranoside × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
7NHP Structure of PSII-I (PSII with Psb27, Psb28, and Psb34) Deposited 2021-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain 2 1–116（116 aa）	Not recorded	MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1 PHO PHEOPHYTIN A × 2 CLA CHLOROPHYLL A × 35 BCR BETA-CAROTENE × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 7 FE FE (III) ION × 1 PL9 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 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.72 Å
7NHQ Structure of PSII-I prime (PSII with Psb28, and Psb34) Deposited 2021-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain 2 1–116（116 aa）	Not recorded	FE FE (III) ION × 1 MN MANGANESE (II) ION × 1 CL CHLORIDE ION × 1 PHO PHEOPHYTIN A × 2 CLA CHLOROPHYLL A × 35 BCR BETA-CAROTENE × 10 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 7 PL9 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 × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.68 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PSB28_THEEB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–133； UniProt 2–116 Author chain B； PDBConstruct 19–133； UniProt 2–116 Author chain C； PDBConstruct 19–133； UniProt 2–116 Author chain D； PDBConstruct 19–133； UniProt 2–116

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3zpn
Deposition date deposition_date	2013-02-28
Structure title title	Structure of Psb28
Keywords keywords	PHOTOSYNTHESIS, PHOTOSYSTEM II ASSEMBLY; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.53 Å
Radius of gyration Rg (electron density) rg_electron	23.37 Å
Forward intensity I(0) i0	42185200.00
Molecular weight molecular_weight	48580.0 kDa
Excluded volume excluded_volume	60043 Å³
Envelope volume envelope_volume	76387 Å³
Hydration-shell volume shell_volume	26966 Å³
Envelope diameter envelope_diameter	72.5 Å
Shell Rg shell_rg	30.45 Å
Envelope Rg envelope_rg	22.98 Å
Shape Rg shape_rg	23.36 Å
Total Rg total_rg	24.20 Å
Total atoms total_atoms	3413
Residues n_residues	427
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.1 Å
Rg (real space) rg_real	24.37 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	4.2190e+07
I(0) uncertainty (real space) i0_real_error	5.4840e+05
Rg (reciprocal space) rg_reciprocal	24.41 Å
I(0) (reciprocal space) i0_reciprocal	42190000.0000
Solution quality estimate total_estimate	0.8419
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.7 Å
Skewness Skewness skewness	0.097
Kurtosis Kurtosis kurtosis	-0.644
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9762000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.983; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3zpnA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	220 — Photosystem II Psb28

Domain ID domain_id	3zpnB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	220 — Photosystem II Psb28

Domain ID domain_id	3zpnC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	220 — Photosystem II Psb28

Domain ID domain_id	3zpnD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	220 — Photosystem II Psb28

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8. Citations (1)

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Unit-cell length a length_a	57.060 Å
Unit-cell length b length_b	57.060 Å
Unit-cell length c length_c	183.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.361 Å
Low-resolution limit resolution_low	57.060 Å
R factor r_factor	0.1945
R_work r_work	0.1925
R_free r_free	0.2342

Description description	PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN
Molecular weight formula_weight	15085.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3466

Structure of Psb28

1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	THERMOSYNECHOCOCCUS ELONGATUS
NCBI Class编号 ncbi_taxonomy_id	146786
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

fit	/app/data/saxs_computation/zp/3zpn/3zpn.fit
pddf	/app/data/pr_computation/zp/3zpn/3zpn.pr.out
profile	/app/data/saxs_computation/zp/3zpn/3zpn.dat