SAXSdb — 1b8d

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

PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 1–164 Chain K； UniProt 1–164	Not recorded	PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN)) × 6 （O36004） PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN)) × 3 PEB PHYCOERYTHROBILIN × 24 PUB PHYCOUROBILIN × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；700MM SODIUM ACETATE,5MM KCL,100MM IMIDAZOLE, PH 7.5 AT 17C	Resolution 1.90 Å R-free 0.227

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	PHEA_GRIMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 1–164 Author chain K； PDBConstruct 1–164； UniProt 1–164

PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))

OrganismNot specified

UniProt O36004

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 × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain B； UniProt 1–177 Chain L； UniProt 1–177	Non-standard monomer：Yes (specific site not provided by mmCIF)	PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN)) × 6 （O36005） PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN)) × 3 PEB PHYCOERYTHROBILIN × 24 PUB PHYCOUROBILIN × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；700MM SODIUM ACETATE,5MM KCL,100MM IMIDAZOLE, PH 7.5 AT 17C	Resolution 1.90 Å R-free 0.227

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	PHEB_GRIMO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–177； UniProt 1–177 Author chain L； PDBConstruct 1–177； UniProt 1–177

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	1b8d
Deposition date deposition_date	1999-01-29
Structure title title	CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN
Keywords keywords	LIGHT-HARVESTING COMPLEX, RED ALGAE, PHYCOBILIPROTEIN, PHOTOSYNTHESIS; 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	28.94 Å
Radius of gyration Rg (electron density) rg_electron	28.26 Å
Forward intensity I(0) i0	99904200.00
Molecular weight molecular_weight	78629.0 kDa
Excluded volume excluded_volume	98216 Å³
Envelope volume envelope_volume	114930 Å³
Hydration-shell volume shell_volume	34059 Å³
Envelope diameter envelope_diameter	102.2 Å
Shell Rg shell_rg	35.41 Å
Envelope Rg envelope_rg	28.28 Å
Shape Rg shape_rg	28.26 Å
Total Rg total_rg	28.91 Å
Total atoms total_atoms	6735
Residues n_residues	685
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	95.6 Å
Rg (real space) rg_real	28.91 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	9.9900e+07
I(0) uncertainty (real space) i0_real_error	1.5560e+06
Rg (reciprocal space) rg_reciprocal	28.92 Å
I(0) (reciprocal space) i0_reciprocal	99910000.0000
Solution quality estimate total_estimate	0.8945
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.302
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25670000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))
Molecular weight formula_weight	17687.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,K
Atom count atom_count	7734

MKSVITTTISAADAAGRFPSSSDLESIQGNIQRAAARLEAAQKLSGNHEAVVKEAGDACFAKYSYLKNAGEAGDSPEKINKCYRDIDHYMRLINYSLVVGGTGPVDEWGIAGSREVYRALNLPGSAYIAAFTFTRDRLCVPRDMSSQAGVEFTSALDYVINSLC

Entity 2 Entity 2 polymer

Description description	PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
Molecular weight formula_weight	18511.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,L

MLDAFSRVVVTSDAKAAYVGGSDLQSLKSFINDGNKRLDAVNYIVSNASCIVSDAVSGMICENPGLIAPGGNCYTNRRMAACLRDGEIILRYVSYALLAGDSSVLDDRCLNGLKETYIALGVPTASSSRAVSIMKATATAFITNTASGRKVEVAAGDCQALQAEAASYFDKVGSSID

Entity 3 Entity 3 polymer

Description description	PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))
Molecular weight formula_weight	656.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GYXXYX

Entity 4 Entity 4 non-polymer

Description description	PHYCOERYTHROBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	PHYCOUROBILIN
Molecular weight formula_weight	590.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	333

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1b8da_
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	d1b8db_
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	d1b8dk_
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	d1b8dl_
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

CATH v4.4 (4 domains)

Domain ID domain_id	1b8dA00
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	1b8dB00
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	1b8dK00
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	1b8dL00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	20 — Phycocyanins

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8. Citations (1)

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Unit-cell length a length_a	187.350 Å
Unit-cell length b length_b	187.350 Å
Unit-cell length c length_c	59.310 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	0.1750
R_free r_free	0.2270

fit	/app/data/saxs_computation/b8/1b8d/1b8d.fit
pddf	/app/data/pr_computation/b8/1b8d/1b8d.pr.out
profile	/app/data/saxs_computation/b8/1b8d/1b8d.dat

CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN

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

PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)