SAXSdb — 3agc

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

Red chlorophyll catabolite reductase, chloroplastic

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;3-{(2Z,3S,4S)-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-2-[(5R)-2-[(3-ethyl-5-formyl-4-methyl-1H-pyrrol-2-yl)methyl]-5-(methoxycarbonyl)-3-methyl-4-oxo-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene]-4-methyl-3,4-dihydro-2H-pyrrol-3-yl}propanoic acid ; × 1 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCCR_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–276； UniProt 49–319 Author chain B； PDBConstruct 6–276； UniProt 49–319

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	3agc
Deposition date deposition_date	2010-03-30
Structure title title	F218V mutant of the substrate-bound red chlorophyll catabolite reductase from Arabidopsis thaliana
Keywords keywords	chlorophyll degradation, substrate-bound enzyme, Chlorophyll catabolism, Chloroplast, NADP, Oxidoreductase, Transit peptide; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3agc__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3agc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3agc__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.51 Å
Rg (electron density)	25.26 Å
Total Rg	26.14 Å
Atom count	4273
Residues	531
Excluded volume	76302 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3agc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Red chlorophyll catabolite reductase, chloroplastic
Molecular weight formula_weight	31347.8 kDa
EC 编号 ec_number	1.3.1.80
Mutation mutation	F218V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4601

GPLGSRRKFMEFPYVSPTRKQLMVDLMSTVENRLQSQLLPCNLPPDVRNFNNPNGSAEASLHIRSGDKSSPIDFVIGSWIHCKIPTGVSLNITSISGFLNSSTKAPNFVVELIQSSSKSLVLILDLPHRKDLVLNPDYLKEYYQDTALDSHRQSLLKLPEVNPYVSPSLFVRSAVSPTASMLKIDAEEEDKLEEILRDHVSPAAKEVLEVWLERCVKEEEEKIVVGEEERMELERRDKSFRRKSIEDDLDLQFPRMFGEEVSSRVVHAIKEAFGVL

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress, thale-cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;3-{(2Z,3S,4S)-5-[(Z)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-2-[(5R)-2-[(3-ethyl-5-formyl-4-methyl-1H-pyrrol-2-yl)methyl]-5-(methoxycarbonyl)-3-methyl-4-oxo-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene]-4-methyl-3,4-dihydro-2H-pyrrol-3-yl}propanoic acid ;
Molecular weight formula_weight	626.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	315

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3agcA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3agcB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1500 — oxygen-dependent coproporphyrinogen oxidase
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	45.089 Å
Unit-cell length b length_b	84.321 Å
Unit-cell length c length_c	131.518 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	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2118
R_work r_work	0.2089
R_free r_free	0.2699

F218V mutant of the substrate-bound red chlorophyll catabolite reductase from Arabidopsis thaliana

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

Red chlorophyll catabolite reductase, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3agc__assembly_1__model_1

3agc__assembly_1__model_1 | I(q)

3agc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

F218V mutant of the substrate-bound red chlorophyll catabolite reductase from Arabidopsis thaliana

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

Red chlorophyll catabolite reductase, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3agc__assembly_1__model_1

3agc__assembly_1__model_1 | I(q)

3agc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)