SAXSdb — 3g23

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

LD-carboxypeptidase A

Novosphingobium aromaticivorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 17 GLYCEROL × 8 UNKNOWN LIGAND × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2G8F3_NOVAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–274； UniProt 1–273 Author chain B； PDBConstruct 2–274； UniProt 1–273

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	3g23
Deposition date deposition_date	2009-01-30
Structure title title	Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium aromaticivorans dsm at 1.89 A resolution
Keywords keywords	;Flavodoxin-like fold, catalytic triad, merops s66 unassigned peptidases family, the swivelling beta/beta/alpha domain fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, hydrolase ;; HYDROLASE
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.

3g23__assembly_1__model_1

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

Download this curve (.dat)

3g23__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3g23__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.72 Å
Rg (electron density)	24.95 Å
Total Rg	25.66 Å
Atom count	4163
Residues	528
Excluded volume	73243 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3g23__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	LD-carboxypeptidase A
Molecular weight formula_weight	29685.8 kDa
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	4681

GMTRRIAICAPSTPFTREDSARVIALAAAEFPDLSLSFHEQCFASEGHFAGSDALRLSAFLECANDDAFEAVWFVRGGYGANRIAEDALARLGRAASAKQYLGYSDAGTLLAALYAHRIGRSVHAPMPVDIRRPEGESAVRRTLGWLAGAREGLEPTLGAGAPAVAFNLMTLAMLCGTRLLPDLSGHVVMIEEVAEHHYAVDRLLFHVTSCLADAGIAGLRLGRVSDVPENDRPFGCSVEEMARHWCHRAGIAFLGTADIGHDVDNRIVPFGLA

Source Source

Source organism organism	Novosphingobium aromaticivorans
NCBI taxonomy ID ncbi_taxonomy_id	279238
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 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	3g23A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10740 — Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain

Domain ID domain_id	3g23A02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	60 — LD-carboxypeptidase A C-terminal domain-like

Domain ID domain_id	3g23B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10740 — Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain

Domain ID domain_id	3g23B02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	60 — LD-carboxypeptidase A C-terminal domain-like

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Unit-cell length a length_a	43.628 Å
Unit-cell length b length_b	91.042 Å
Unit-cell length c length_c	145.744 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	29.709 Å
R factor r_factor	0.1730
R_work r_work	0.1710
R_free r_free	0.2070

Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium aromaticivorans dsm at 1.89 A resolution

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

LD-carboxypeptidase A

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

3g23__assembly_1__model_1

3g23__assembly_1__model_1 | I(q)

3g23__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium aromaticivorans dsm at 1.89 A resolution

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

LD-carboxypeptidase A

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

3g23__assembly_1__model_1

3g23__assembly_1__model_1 | I(q)

3g23__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)