1gg4

CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION

Method: X-RAY DIFFRACTION

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

UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE

Escherichia coli

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–452； UniProt 1–452 Author chain B； PDBConstruct 1–452； UniProt 1–452

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	1gg4
Deposition date deposition_date	2000-07-12
Structure title title	CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION
Keywords keywords	alpha/beta sheet, LIGASE; LIGASE
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.

1gg4__assembly_1__model_1

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

Download this curve (.dat)

1gg4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1gg4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.28 Å
Rg (electron density)	25.63 Å
Total Rg	26.22 Å
Atom count	3242
Residues	430
Excluded volume	57998 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1gg4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1gg4__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Description description	UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE
Molecular weight formula_weight	47910.9 kDa
EC 编号 ec_number	6.3.2.15
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	6791

MISVTLSQLTDILNGELQGADITLDAVTTDTRKLTPGCLFVALKGERFDAHDFADQAKAGGAGALLVSRPLDIDLPQLIVKDTRLAFGELAAWVRQQVPARVVALTGSSGKTSVKEMTAAILSQCGNTLYTAGNLNNDIGVPMTLLRLTPEYDYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFSGLPENGIAIMNADNNDWLNWQSVIGSRKVWRFSPNAANSDFTATNIHVTSHGTEFTLQTPTGSVDVLLPLPGRHNIANALAAAALSMSVGATLDAIKAGLANLKAVPGRLFPIQLAENQLLLDDSYNANVGSMTAAVQVLAEMPGYRVLVVGDMAELGAESEACHVQVGEAAKAAGIDRVLSVGKQSHAISTASGVGEHFADKTALITRLKLLIAEQQVITILVKGSRSAAMEEVVRALQENGTC

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	307

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1gg4a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.59 — MurD-like peptide ligases, peptide-binding domain
Superfamily Superfamily superfamily	c.59.1 — MurD-like peptide ligases, peptide-binding domain
Family Family family	c.59.1.1 — MurCDEF C-terminal domain

Domain ID domain_id	d1gg4a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.1 — MurE/MurF N-terminal domain
Family Family family	c.98.1.1 — MurE/MurF N-terminal domain

Domain ID domain_id	d1gg4a4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.1 — MurCDEF

Domain ID domain_id	d1gg4b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.59 — MurD-like peptide ligases, peptide-binding domain
Superfamily Superfamily superfamily	c.59.1 — MurD-like peptide ligases, peptide-binding domain
Family Family family	c.59.1.1 — MurCDEF C-terminal domain

Domain ID domain_id	d1gg4b3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.98 — MurF and HprK N-domain-like
Superfamily Superfamily superfamily	c.98.1 — MurE/MurF N-terminal domain
Family Family family	c.98.1.1 — MurE/MurF N-terminal domain

Domain ID domain_id	d1gg4b4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.2 — MurD-like peptide ligases, catalytic domain
Family Family family	c.72.2.1 — MurCDEF

CATH v4.4 (6 domains)

Domain ID domain_id	1gg4A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	20 — Mur ligase, C-terminal domain

Domain ID domain_id	1gg4A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	1gg4A03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

Domain ID domain_id	1gg4B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	20 — Mur ligase, C-terminal domain

Domain ID domain_id	1gg4B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	10 — Mur-like, catalytic domain

Domain ID domain_id	1gg4B03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — MurE/MurF, N-terminal domain

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Unit-cell length a length_a	74.200 Å
Unit-cell length b length_b	74.200 Å
Unit-cell length c length_c	429.300 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2030
R_free r_free	0.2800

CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION

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

UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE

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

1gg4__assembly_1__model_1

1gg4__assembly_1__model_1 | I(q)

1gg4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION

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

UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE

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

1gg4__assembly_1__model_1

1gg4__assembly_1__model_1 | I(q)

1gg4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)