SAXSdb — 3cqy

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

Anhydro-N-acetylmuramic acid kinase

Shewanella oneidensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 3 SUCCINIC ACID × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 3 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 12 SUCCINIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ANMK_SHEON
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–370； UniProt 1–369 Author chain B； PDBConstruct 2–370； UniProt 1–369

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	3cqy
Deposition date deposition_date	2008-04-03
Structure title title	Crystal structure of a functionally unknown protein (SO_1313) from Shewanella oneidensis MR-1
Keywords keywords	;APC7501, SO_1313, structural genomics, PSI-2, Shewanella oneidensis MR-1, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, ATP-binding, Carbohydrate metabolism, Kinase, Nucleotide-binding, Transferase ;; TRANSFERASE
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.

3cqy__assembly_1__model_1

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

Download this curve (.dat)

3cqy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cqy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.43 Å
Rg (electron density)	20.31 Å
Total Rg	21.29 Å
Atom count	2829
Residues	364
Excluded volume	50547 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cqy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cqy__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cqy__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	Anhydro-N-acetylmuramic acid kinase
Molecular weight formula_weight	40185.7 kDa
EC 编号 ec_number	2.7.1.-
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	6096

GMNKAYYIGLMSGTSMDGVDAVLVDFAGEQPQLIGTHTETIPTHLLKGLQRLCLPGTDEINRLGRLDRSVGKLFALAVNNLLAKTKIAKDEIIAIGSHGQTVRHMPNLEVGFTLQIGDPNTIATETGIDVIADFRRKDIALGGQGAPLVPAFHQQTFAQVGKKRVILNIGGIANITYLPGNSEEVLGFDTGPGNTLIDAWVQQVKNESYDKNGAWAASGKTDPQLLAQLLSHPYFSLAYPKSTGRELFNQAWLEQQLSAFNQLNEEDIQSTLLDLTCHSIAQDILKLAQEGELFVCGGGAFNAELMQRLAALLPGYRIDTTSALGVDPKWAEGIAFAWLAMRYQLGLPANLPAVTGASREAILGGRFSAK

Source Source

Source organism organism	Shewanella oneidensis
NCBI taxonomy ID ncbi_taxonomy_id	211586
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	450

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3cqyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3cqyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3cqyB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3cqyB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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Unit-cell length a length_a	147.816 Å
Unit-cell length b length_b	147.816 Å
Unit-cell length c length_c	117.687 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	47.780 Å
R factor r_factor	0.1746
R_work r_work	0.1727
R_free r_free	0.2112

Crystal structure of a functionally unknown protein (SO_1313) from Shewanella oneidensis MR-1

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

Anhydro-N-acetylmuramic acid kinase

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

3cqy__assembly_1__model_1

3cqy__assembly_1__model_1 | I(q)

3cqy__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a functionally unknown protein (SO_1313) from Shewanella oneidensis MR-1

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

Anhydro-N-acetylmuramic acid kinase

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

3cqy__assembly_1__model_1

3cqy__assembly_1__model_1 | I(q)

3cqy__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)