SAXSdb — 1vzm

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

OSTEOCALCIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OSTCN_ARGRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–45； UniProt 53–97 Author chain B； PDBConstruct 1–45； UniProt 53–97 Author chain C； PDBConstruct 1–45； UniProt 53–97

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	1vzm
Deposition date deposition_date	2004-05-21
Structure title title	OSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS
Keywords keywords	;CALCIUM-BINDING PROTEIN, OSTEOCALCIN, BONE GLA PROTEIN, BGP, HYDROXYAPATITE, GAMMA CARBOXYL GLUTAMIC ACID, VITAMIN K, BONE, MINERALIZATION ;; CALCIUM-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.

1vzm__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vzm__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vzm__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	10.65 Å
Rg (electron density)	9.45 Å
Total Rg	10.93 Å
Atom count	335
Residues	38
Excluded volume	5903 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vzm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vzm__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1vzm__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 (3)

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1vzma_
Class class	g — Small proteins
Fold Fold fold	g.32 — GLA-domain
Superfamily Superfamily superfamily	g.32.1 — GLA-domain
Family Family family	g.32.1.0 — automated matches

Domain ID domain_id	d1vzmb_
Class class	g — Small proteins
Fold Fold fold	g.32 — GLA-domain
Superfamily Superfamily superfamily	g.32.1 — GLA-domain
Family Family family	g.32.1.0 — automated matches

Domain ID domain_id	d1vzmc_
Class class	g — Small proteins
Fold Fold fold	g.32 — GLA-domain
Superfamily Superfamily superfamily	g.32.1 — GLA-domain
Family Family family	g.32.1.0 — automated matches

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Unit-cell length a length_a	48.700 Å
Unit-cell length b length_b	48.700 Å
Unit-cell length c length_c	119.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	39.750 Å
R factor r_factor	0.1916
R_work r_work	—
R_free r_free	0.2346

Description description	OSTEOCALCIN
Molecular weight formula_weight	5046.5 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1241

OSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS

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

OSTEOCALCIN

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

1vzm__assembly_2__model_1

1vzm__assembly_2__model_1 | I(q)

1vzm__assembly_2__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (2)

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

OSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS

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

OSTEOCALCIN

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

1vzm__assembly_2__model_1

1vzm__assembly_2__model_1 | I(q)

1vzm__assembly_2__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (2)