SAXSdb — 4g86

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

Circadian clock protein kaiA

Synechococcus elongatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 4 PENTAETHYLENE GLYCOL × 1 NONAETHYLENE GLYCOL × 1 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIA_SYNE7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–284； UniProt 2–284 Author chain B； PDBConstruct 2–284； UniProt 2–284

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	4g86
Deposition date deposition_date	2012-07-21
Structure title title	Crystal structure of the redox-active cofactor DBMIB bound to the full length circadian clock protein KaiA from Synechococcus elongatus
Keywords keywords	homodimer, KaiC phosphorylation activator, KaiC, PROTEIN BINDING; PROTEIN BINDING
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.

4g86__assembly_1__model_1

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

Download this curve (.dat)

4g86__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4g86__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.27 Å
Rg (electron density)	27.23 Å
Total Rg	28.10 Å
Atom count	4632
Residues	564
Excluded volume	82520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4g86__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 (6)

Entity 1 Entity 1 polymer

Description description	Circadian clock protein kaiA
Molecular weight formula_weight	32634.1 kDa
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	4809

VLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDRDSEDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMADHIMLMGANHDPELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPRET

Source Source

Source organism organism	Synechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	1140
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE
Molecular weight formula_weight	322.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	177

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4g86A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	4g86A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
Homologous superfamily homologous superfamily	30 — KaiA/RbsU domain

Domain ID domain_id	4g86B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	4g86B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
Homologous superfamily homologous superfamily	30 — KaiA/RbsU domain

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Unit-cell length a length_a	47.247 Å
Unit-cell length b length_b	126.354 Å
Unit-cell length c length_c	56.383 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.387 Å
Low-resolution limit resolution_low	47.582 Å
R factor r_factor	0.2210
R_work r_work	0.2187
R_free r_free	0.2650

Crystal structure of the redox-active cofactor DBMIB bound to the full length circadian clock protein KaiA from Synechococcus elongatus

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

Circadian clock protein kaiA

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

4g86__assembly_1__model_1

4g86__assembly_1__model_1 | I(q)

4g86__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the redox-active cofactor DBMIB bound to the full length circadian clock protein KaiA from Synechococcus elongatus

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

Circadian clock protein kaiA

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

4g86__assembly_1__model_1

4g86__assembly_1__model_1 | I(q)

4g86__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)