SAXSdb — 3gkr

▼

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

FemX

Lactobacillus viridescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	UDP-MurNAc-peptide × 1 MAGNESIUM ION × 3 GLYCEROL × 1 ALANINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9EY50_LACVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–336； UniProt 1–336

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3gkr
Deposition date deposition_date	2009-03-11
Structure title title	Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexapeptide complex
Keywords keywords	FEMX, PEPTIDOGLYCAN, HEXAPEPTIDE, transferase, Transferase-Transferase Product complex; Transferase/Transferase Product
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3gkr__assembly_1__model_1

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

Download this curve (.dat)

3gkr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gkr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.60 Å
Rg (electron density)	20.51 Å
Total Rg	21.36 Å
Atom count	2778
Residues	336
Excluded volume	49158 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gkr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	FemX
Molecular weight formula_weight	38327.0 kDa
EC 编号 ec_number	2.3.2.10
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3292

MPVLNLNDPQAVERYEEFMRQSPYGQVTQDLGWAKVKNNWEPVDVYLEDDQGAIIAAMSMLLGDTPTDKKFAYASKGPVMDVTDVDLLDRLVDEAVKALDGRAYVLRFDPEVAYSDEFNTTLQDHGYVTRNRNVADAGMHATIQPRLNMVLDLTKFPDAKTTLDLYPSKTKSKIKRPFRDGVEVHSGNSATELDEFFKTYTTMAERHGITHRPIEYFQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALDTNTDLYDLGGIESESTDDSLYVFKHVFVKDAPREYIGEIDKVLDPEVYAELVKD

Source Source

Source organism organism	Lactobacillus viridescens
NCBI taxonomy ID ncbi_taxonomy_id	1629
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	UDP-MurNAc-peptide
Molecular weight formula_weight	1150.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AEKAA

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	ALANINE
Molecular weight formula_weight	89.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	514

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3gkrA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	3gkrA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

▶

Unit-cell length a length_a	42.324 Å
Unit-cell length b length_b	101.836 Å
Unit-cell length c length_c	46.847 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	27.200 Å
R factor r_factor	0.1751
R_work r_work	0.1730
R_free r_free	0.2156

Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexapeptide complex

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

FemX

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

3gkr__assembly_1__model_1

3gkr__assembly_1__model_1 | I(q)

3gkr__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexapeptide complex

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

FemX

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

3gkr__assembly_1__model_1

3gkr__assembly_1__model_1 | I(q)

3gkr__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)