SAXSdb — 2z1c

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

Hydrogenase expression/formation protein HypC

Thermococcus kodakarensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	TETRAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5JII0_PYRKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–75； UniProt 1–75 Author chain B； PDBConstruct 1–75； UniProt 1–75 Author chain C； PDBConstruct 1–75； UniProt 1–75

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	2z1c
Deposition date deposition_date	2007-05-08
Structure title title	Crystal structure of HypC from Thermococcus kodakaraensis KOD1
Keywords keywords	[NiFe] hydrogenase maturation, OB-fold, CHAPERONE, METAL BINDING PROTEIN; CHAPERONE, METAL BINDING PROTEIN
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.

2z1c__assembly_1__model_1

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

Download this curve (.dat)

2z1c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2z1c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	13.79 Å
Rg (electron density)	12.53 Å
Total Rg	13.87 Å
Atom count	541
Residues	71
Excluded volume	9820 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2z1c__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2z1c__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2z1c__assembly_3__model_1`	monomeric （1）	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	Hydrogenase expression/formation protein HypC
Molecular weight formula_weight	8264.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1726

MCLAVPGKVIEVNGPVAVVDFGGVKREVRLDLMPDTKPGDWVIVHTGFAIEKLDEKKAMEILEAWAEVEKAMEGF

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 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 (3 domains)

Domain ID domain_id	d2z1ca1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.14 — HupF/HypC-like
Family Family family	b.40.14.1 — HupF/HypC-like

Domain ID domain_id	d2z1cb_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.14 — HupF/HypC-like
Family Family family	b.40.14.1 — HupF/HypC-like

Domain ID domain_id	d2z1cc_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.14 — HupF/HypC-like
Family Family family	b.40.14.1 — HupF/HypC-like

CATH v4.4 (3 domains)

Domain ID domain_id	2z1cA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2z1cB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2z1cC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

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Unit-cell length a length_a	78.237 Å
Unit-cell length b length_b	59.130 Å
Unit-cell length c length_c	53.973 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	46.180 Å
R factor r_factor	0.2230
R_work r_work	0.2220
R_free r_free	0.2460

Crystal structure of HypC from Thermococcus kodakaraensis KOD1

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

Hydrogenase expression/formation protein HypC

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

2z1c__assembly_1__model_1

2z1c__assembly_1__model_1 | I(q)

2z1c__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of HypC from Thermococcus kodakaraensis KOD1

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

Hydrogenase expression/formation protein HypC

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

2z1c__assembly_1__model_1

2z1c__assembly_1__model_1 | I(q)

2z1c__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)