7z5y

CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE

Method: X-RAY DIFFRACTION

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

UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase

Weissella viridescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 1	;HNA (5'-D(P(6HA)P(6HC)P(6HC))-R(P(A9Z))-3') ; × 1 UDP-MurNAc-pentapeptide × 1 GLYCEROL × 1 URIDINE-5'-DIPHOSPHATE × 1 N-acetyl-alpha-muramic acid × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FEMX_WEIVI
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7z5y
Deposition date deposition_date	2022-03-10
Structure title title	CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE
Keywords keywords	FEMX, Xeno-nucleic acids, PEPTIDOGLYCAN, TRANSFERASE, PEPTIDYL-XNA CONJUGATE, TRANSFERASE-PEPTIDE-XNA COMPLEX; 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.

7z5y__assembly_1__model_1

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

Download this curve (.dat)

7z5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7z5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.67 Å
Rg (electron density)	20.54 Å
Total Rg	21.39 Å
Atom count	2862
Residues	338
Excluded volume	50348 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7z5y__assembly_1__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase
Molecular weight formula_weight	39212.9 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	2996

MPVLNLNDPQAVERYEEFMRQSPYGQVTQDLGWAKVKNNWEPVDVYLEDDQGAIIAAMSMLLGDTPTDKKFAYASKGPVMDVTDVDLLDRLVDEAVKALDGRAYVLRFDPEVAYSDEFNTTLQDHGYVTRNRNVADAGMHATIQPRLNMVLDLTKFPDAKTTLDLYPSKTKSKIKRPFRDGVEVHSGNSATELDEFFKTYTTMAERHGITHRPIEYFQRMQAAFDADTMRIFVAEREGKLLSTGIALKYGRKIWYMYAGSMDGNTYYAPYAVQSEMIQWALDTNTDLYDLGGIESESTDDSLYVFKHVFVKDAPREYIGEIDKVLDPEVYAELVKDGHHHHHH

Source Source

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

Entity 2 Entity 2 polymer

Description description	;HNA (5'-D(P(6HA)P(6HC)P(6HC))-R(P(A9Z))-3') ;
Molecular weight formula_weight	1297.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ACCX

Entity 3 Entity 3 polymer

Description description	UDP-MurNAc-pentapeptide
Molecular weight formula_weight	463.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

AECAA

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	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	N-acetyl-alpha-muramic acid
Molecular weight formula_weight	293.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	134

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Unit-cell length a length_a	42.160 Å
Unit-cell length b length_b	101.960 Å
Unit-cell length c length_c	46.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.78 °
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	1.710 Å
Low-resolution limit resolution_low	41.200 Å
R factor r_factor	0.2134
R_work r_work	0.2119
R_free r_free	0.2415

CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE

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

UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase

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

7z5y__assembly_1__model_1

7z5y__assembly_1__model_1 | I(q)

7z5y__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE

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

UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase

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

7z5y__assembly_1__model_1

7z5y__assembly_1__model_1 | I(q)

7z5y__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)