SAXSdb — 5jwr

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

Circadian clock protein kinase KaiC

Thermosynechococcus elongatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Circadian clock protein KaiB × 1 （Q79V61） Circadian clock protein KaiA × 2 （Q79V62） PHOSPHATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Circadian clock protein KaiB × 1 （Q79V61） Circadian clock protein KaiA × 2 （Q79V62） PHOSPHATE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIC_THEEB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–239； UniProt 17–247 Author chain C； PDBConstruct 9–239； UniProt 17–247

Circadian clock protein KaiB

Thermosynechococcus elongatus (strain BP-1)

UniProt Q79V61

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Circadian clock protein kinase KaiC × 1 （Q79V60） Circadian clock protein KaiA × 2 （Q79V62） PHOSPHATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Circadian clock protein kinase KaiC × 1 （Q79V60） Circadian clock protein KaiA × 2 （Q79V62） PHOSPHATE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIB_THEEB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 1–99 Author chain D； PDBConstruct 1–99； UniProt 1–99

Circadian clock protein KaiA

Thermosynechococcus elongatus

UniProt Q79V62

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Circadian clock protein kinase KaiC × 1 （Q79V60） Circadian clock protein KaiB × 1 （Q79V61） PHOSPHATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Circadian clock protein kinase KaiC × 1 （Q79V60） Circadian clock protein KaiB × 1 （Q79V61） PHOSPHATE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIA_THEEB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 9–145； UniProt 147–283 Author chain F； PDBConstruct 9–145； UniProt 147–283 Author chain G； PDBConstruct 9–145； UniProt 147–283 Author chain H； PDBConstruct 9–145； UniProt 147–283

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	5jwr
Deposition date deposition_date	2016-05-12
Structure title title	Crystal structure of foldswitch-stabilized KaiB in complex with the N-terminal CI domain of KaiC and a dimer of KaiA C-terminal domains from Thermosynechococcus elongatus
Keywords keywords	Transcription Regulator, foldswitch; Transcription Regulator
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.

5jwr__assembly_1__model_1

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

Download this curve (.dat)

5jwr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jwr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.07 Å
Rg (electron density)	28.13 Å
Total Rg	28.87 Å
Atom count	4763
Residues	586
Excluded volume	85638 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jwr__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5jwr__assembly_2__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	Circadian clock protein kinase KaiC
Molecular weight formula_weight	27738.2 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	R41A, K173A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	9528

DYKDDDDKAEVKKIPTMIEGFDDISHGGLPQGATTLVSGTSGTGKTLFAVQFLYNGITIFNEPGIFVTFEESPQDIIKNALSFGWNLQSLIDQGKLFILDASPDPDGQEVAGDFDLSALIERIQYAIRKYKATRVSIDSVTAVFQQYDAASVVRREIFRLAFRLAQLGVTTIMTTERVDEYGPVARFGVEEFVSDNVVILRNVLEGERRRRTVEILKLRGTTHMKGEYPFTINNGINIFDYKDDDDK

Source Source

Source organism organism	Thermosynechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	197221
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Circadian clock protein KaiB
Molecular weight formula_weight	10941.0 kDa
Mutation mutation	Y8A, G89A, D91R, Y94A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAPLRKTAVLKLYVAGNTPNSVRALKTLNNILEKEFKGVYALKVIDVLKNPQLAEEDKILATPTLAKVLPPPVRRIIGDLSNREKVLIALRLLAEEIGD

Source Source

Source organism organism	Thermosynechococcus elongatus (strain BP-1)
NCBI taxonomy ID ncbi_taxonomy_id	197221
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Circadian clock protein KaiA
Molecular weight formula_weight	17332.8 kDa
Mutation mutation	C272S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

DYKDDDDKSNVDPQHRLSQKLKERLGYLGVYYKRDTAFFFRRMSPADKRKLLDELRSIYRTIVLEYFNTDAKVNERIDEFVSKAFFADISVSQVLEIHVELMDTFSKQLKLEGRSEDILLDYRLTLIDVIAHLSEMYRRSIPREV

Source Source

Source organism organism	Thermosynechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	197221
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	106

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5jwrb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.15 — KaiB-like

Domain ID domain_id	d5jwrd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.15 — KaiB-like

CATH v4.4 (4 domains)

Domain ID domain_id	5jwrA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5jwrB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5jwrC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5jwrD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	74.595 Å
Unit-cell length b length_b	79.105 Å
Unit-cell length c length_c	80.838 Å
Unit-cell angle α angle_alpha	107.27 °
Unit-cell angle β angle_beta	90.71 °
Unit-cell angle γ angle_gamma	111.20 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.610 Å
Low-resolution limit resolution_low	44.841 Å
R factor r_factor	0.1876
R_work r_work	0.1847
R_free r_free	0.2420

Crystal structure of foldswitch-stabilized KaiB in complex with the N-terminal CI domain of KaiC and a dimer of KaiA C-terminal domains from Thermosynechococcus elongatus

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

Circadian clock protein kinase KaiC

State in the Current Structure

Other States of the Same Protein in the Database

Circadian clock protein KaiB

State in the Current Structure

Other States of the Same Protein in the Database

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

5jwr__assembly_1__model_1

5jwr__assembly_1__model_1 | I(q)

5jwr__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of foldswitch-stabilized KaiB in complex with the N-terminal CI domain of KaiC and a dimer of KaiA C-terminal domains from Thermosynechococcus elongatus

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

Circadian clock protein kinase KaiC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Circadian clock protein KaiB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

5jwr__assembly_1__model_1

5jwr__assembly_1__model_1 | I(q)

5jwr__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)