SAXSdb — 1nr9

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

Protein YCGM

Escherichia coli

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YCGM_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–221； UniProt 1–219 Author chain B； PDBConstruct 3–221； UniProt 1–219 Author chain C； PDBConstruct 3–221； UniProt 1–219 Author chain D； PDBConstruct 3–221； UniProt 1–219

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	1nr9
Deposition date deposition_date	2003-01-24
Structure title title	Crystal Structure of Escherichia coli 1262 (APC5008), Putative Isomerase
Keywords keywords	;Structural Genomics, Putative Isomerase, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1nr9__assembly_1__model_1

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

Download this curve (.dat)

1nr9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nr9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.43 Å
Rg (electron density)	21.21 Å
Total Rg	21.94 Å
Atom count	3207
Residues	413
Excluded volume	57308 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nr9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nr9__assembly_2__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	Protein YCGM
Molecular weight formula_weight	24311.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6697

GHMYQHHNWQGALLDYPVSKVVCVGSNYAKHIKEMGSAVPEEPVLFIKPETALCDLRQPLAIPSDFGSVHHEVELAVLIGATLRQATEEHVRKAIAGYGVALDLTLRDVQGKMKKAGQPWEKAKAFDNSCPLSGFIPAAEFTGDPQNTTLSLSVNGEQRQQGTTADMIHKIVPLIAYMSKFFTLKAGDVVLTGTPDGVGPLQSGDELTVTFDGHSLTTRVLGS

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	277

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1nr9a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nr9a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1nr9a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1nr9b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nr9c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nr9c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1nr9d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nr9d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1nr9A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nr9B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nr9C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nr9D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

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Unit-cell length a length_a	59.373 Å
Unit-cell length b length_b	83.546 Å
Unit-cell length c length_c	94.896 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	47.380 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2750

Crystal Structure of Escherichia coli 1262 (APC5008), Putative Isomerase

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

Protein YCGM

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

1nr9__assembly_1__model_1

1nr9__assembly_1__model_1 | I(q)

1nr9__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Escherichia coli 1262 (APC5008), Putative Isomerase

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

Protein YCGM

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

1nr9__assembly_1__model_1

1nr9__assembly_1__model_1 | I(q)

1nr9__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)