1b33

STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8

Method: X-RAY DIFFRACTION D_max: 172.6 Å Quality: GOOD

▼

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

ALLOPHYCOCYANIN, ALPHA CHAIN

OrganismNot specified

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–160 Chain C； UniProt 1–160 Chain E； UniProt 1–160	Fragment：ALPHA CHAINS	ALLOPHYCOCYANIN, BETA CHAIN × 3 （P00318） PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE × 1 （P20116） CYC PHYCOCYANOBILIN × 6 BO4 BORATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.9；pH 7.9	Resolution 2.30 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain H； UniProt 1–160 Chain J； UniProt 1–160 Chain L； UniProt 1–160	Fragment：ALPHA CHAINS	ALLOPHYCOCYANIN, BETA CHAIN × 3 （P00318） PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE × 1 （P20116） CYC PHYCOCYANOBILIN × 6 BO4 BORATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.9；pH 7.9	Resolution 2.30 Å R-free 0.256

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PHAA_MASLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–160； UniProt 1–160 Author chain C； PDBConstruct 1–160； UniProt 1–160 Author chain E； PDBConstruct 1–160； UniProt 1–160 Author chain H； PDBConstruct 1–160； UniProt 1–160 Author chain J； PDBConstruct 1–160； UniProt 1–160 Author chain L； PDBConstruct 1–160； UniProt 1–160

ALLOPHYCOCYANIN, BETA CHAIN

OrganismNot specified

UniProt P00318

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain B； UniProt 1–161 Chain D； UniProt 1–161 Chain F； UniProt 1–161	Fragment：BETA CHAINS Non-standard monomer：Yes (specific site not provided by mmCIF)	ALLOPHYCOCYANIN, ALPHA CHAIN × 3 （P00315） PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE × 1 （P20116） CYC PHYCOCYANOBILIN × 6 BO4 BORATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.9；pH 7.9	Resolution 2.30 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain I； UniProt 1–161 Chain K； UniProt 1–161 Chain M； UniProt 1–161	Fragment：BETA CHAINS Non-standard monomer：Yes (specific site not provided by mmCIF)	ALLOPHYCOCYANIN, ALPHA CHAIN × 3 （P00315） PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE × 1 （P20116） CYC PHYCOCYANOBILIN × 6 BO4 BORATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.9；pH 7.9	Resolution 2.30 Å R-free 0.256

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PHAB_MASLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–161； UniProt 1–161 Author chain D； PDBConstruct 1–161； UniProt 1–161 Author chain F； PDBConstruct 1–161； UniProt 1–161 Author chain I； PDBConstruct 1–161； UniProt 1–161 Author chain K； PDBConstruct 1–161； UniProt 1–161 Author chain M； PDBConstruct 1–161； UniProt 1–161

PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE

OrganismNot specified

UniProt P20116

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain N； UniProt 1–67	Fragment：PEPTIDE LINKER	ALLOPHYCOCYANIN, ALPHA CHAIN × 3 （P00315） ALLOPHYCOCYANIN, BETA CHAIN × 3 （P00318） CYC PHYCOCYANOBILIN × 6 BO4 BORATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.9；pH 7.9	Resolution 2.30 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain O； UniProt 1–67	Fragment：PEPTIDE LINKER	ALLOPHYCOCYANIN, ALPHA CHAIN × 3 （P00315） ALLOPHYCOCYANIN, BETA CHAIN × 3 （P00318） CYC PHYCOCYANOBILIN × 6 BO4 BORATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.9；pH 7.9	Resolution 2.30 Å R-free 0.256

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PYC1_MASLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 1–67； UniProt 1–67 Author chain O； PDBConstruct 1–67； UniProt 1–67

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b33
Deposition date deposition_date	1998-12-15
Structure title title	STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8
Keywords keywords	LIGHT-HARVESTING PROTEIN, CYANOBACTERIA, ALLOPHYCOCYANIN, LINKER POLYPEPTIDES, COMPLEX STRUCTURE, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	52.26 Å
Radius of gyration Rg (electron density) rg_electron	52.25 Å
Forward intensity I(0) i0	740638000.00
Molecular weight molecular_weight	229910.0 kDa
Excluded volume excluded_volume	289460 Å³
Envelope volume envelope_volume	414420 Å³
Hydration-shell volume shell_volume	68267 Å³
Envelope diameter envelope_diameter	170.3 Å
Shell Rg shell_rg	53.67 Å
Envelope Rg envelope_rg	50.20 Å
Shape Rg shape_rg	52.25 Å
Total Rg total_rg	52.33 Å
Total atoms total_atoms	16158
Residues n_residues	2054
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

▼

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

Maximum dimension Dmax dmax	172.6 Å
Rg (real space) rg_real	52.36 Å
Rg uncertainty (real space) rg_real_error	1.72 Å
I(0) (real space) i0_real	7.4060e+08
I(0) uncertainty (real space) i0_real_error	1.3970e+07
Rg (reciprocal space) rg_reciprocal	52.15 Å
I(0) (reciprocal space) i0_reciprocal	740400000.0000
Solution quality estimate total_estimate	0.8570
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.3 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.507
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30850000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.368

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	ALLOPHYCOCYANIN, ALPHA CHAIN
Molecular weight formula_weight	17138.4 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,H,J,L
Atom count atom_count	17502

SIVTKSIVNADAEARYLSPGELDRIKSFVSSGEKRLRIAQILTDNRERIVKQAGDQLFQKRPDVVSPGGNAYGQEMTATCLRDLDYYLRLITYGIVAGDVTPIEEIGIVGVREMYKSLGTPIDAVAAGVSAMKNVASSILSAEDAAEAGAYFDYVAGALA

Entity 2 Entity 2 polymer

Description description	ALLOPHYCOCYANIN, BETA CHAIN
Molecular weight formula_weight	17403.8 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,I,K,M

MQDAITAVINSSDVQGKYLDTAALEKLKSYFSTGELRVRAATTIAANAAAIVKEAVAKSLLYSDITRPGGNMYTTRRYAACIRDLDYYLRYATYAMLAGDPSILDERVLNGLKETYNSLGVPISATVQAIQAMKEVTASLVGPDAGKEMGVYFDYICSGLS

Entity 3 Entity 3 polymer

Description description	PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE
Molecular weight formula_weight	7753.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,O

GRLFKITACVPSQTRIRTQRELQNTYFTKLVPYENWFREQQRIQKMGGKIVKVELATGKQGINTGLA

Entity 4 Entity 4 non-polymer

Description description	PHYCOCYANOBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 non-polymer

Description description	BORATE ION
Molecular weight formula_weight	78.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1344

▼

7. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d1b33a_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33b_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33c_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33d_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33e_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33f_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33h_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33i_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33j_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33k_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33l_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33m_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.3 — Phycocyanin-like phycobilisome proteins

Domain ID domain_id	d1b33n_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.30 — Allophycocyanin linker chain (domain)
Superfamily Superfamily superfamily	d.30.1 — Allophycocyanin linker chain (domain)
Family Family family	d.30.1.1 — Allophycocyanin linker chain (domain)

Domain ID domain_id	d1b33o_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.30 — Allophycocyanin linker chain (domain)
Superfamily Superfamily superfamily	d.30.1 — Allophycocyanin linker chain (domain)
Family Family family	d.30.1.1 — Allophycocyanin linker chain (domain)

CATH v4.4 (14 domains)

Domain ID domain_id	1b33A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33H00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33I00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33J00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33K00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33L00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33M00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

Domain ID domain_id	1b33N01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	170 — Allophycocyanin linker chain (domain)

Domain ID domain_id	1b33O01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	170 — Allophycocyanin linker chain (domain)

▶

8. Citations (4)

▶

Unit-cell length a length_a	176.120 Å
Unit-cell length b length_b	151.900 Å
Unit-cell length c length_c	137.850 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2560

fit	/app/data/saxs_computation/b3/1b33/1b33.fit
pddf	/app/data/pr_computation/b3/1b33/1b33.pr.out
profile	/app/data/saxs_computation/b3/1b33/1b33.dat

STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8

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

ALLOPHYCOCYANIN, ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

ALLOPHYCOCYANIN, BETA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

CATH v4.4 (14 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)