SAXSdb — 1kcf

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

HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I

Schizosaccharomyces pombe

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCE1_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 1–258 Author chain B； PDBConstruct 1–258； UniProt 1–258

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	1kcf
Deposition date deposition_date	2001-11-08
Structure title title	Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2
Keywords keywords	beta-alpha-beta motif, RuvC resolvase family, HYDROLASE; HYDROLASE
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.

1kcf__assembly_1__model_1

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

Download this curve (.dat)

1kcf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kcf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.26 Å
Rg (electron density)	26.76 Å
Total Rg	27.49 Å
Atom count	3748
Residues	468
Excluded volume	66888 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kcf__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 (3)

Entity 1 Entity 1 polymer

Description description	HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I
Molecular weight formula_weight	30247.8 kDa
EC 编号 ec_number	3.1.-.-
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	3968

MATVKLSFLQHICKLTGLSRSGRKDELLRRIVDSPIYPTSRVLGIDLGIKNFSYCFASQNEDSKVIIHNWSVENLTEKNGLDIQWTEDFQPSSMADLSIQLFNTLHEKFNPHVILMERQRYRSGIATIPEWTLRVNMLESMLYALHYAEKRNSIEQKIQYPFLLSLSPKSTYSYWASVLNTKASFSKKKSRVQMVKELIDGQKILFENEEALYKWNNGSRVEFKKDDMADSALIASGWMRWQAQLKHYRNFCKQFLKQ

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	220

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1kcfa1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.2 — SAP domain
Family Family family	a.140.2.1 — SAP domain

Domain ID domain_id	d1kcfa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.7 — Mitochondrial resolvase ydc2 catalytic domain

Domain ID domain_id	d1kcfb1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.2 — SAP domain
Family Family family	a.140.2.1 — SAP domain

Domain ID domain_id	d1kcfb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.7 — Mitochondrial resolvase ydc2 catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	1kcfA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	1kcfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

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Unit-cell length a length_a	72.000 Å
Unit-cell length b length_b	133.940 Å
Unit-cell length c length_c	73.250 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	2.300 Å
Low-resolution limit resolution_low	29.340 Å
R factor r_factor	0.2420
R_work r_work	0.2380
R_free r_free	0.2700

Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2

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

HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I

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

1kcf__assembly_1__model_1

1kcf__assembly_1__model_1 | I(q)

1kcf__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2

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

HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I

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

1kcf__assembly_1__model_1

1kcf__assembly_1__model_1 | I(q)

1kcf__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)