SAXSdb — 3d0f

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

Penicillin-binding 1 transmembrane protein MrcA

Nitrosomonas europaea ATCC 19718

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q81ZZ3_NITEU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–106； UniProt 318–420 Author chain B； PDBConstruct 4–106； UniProt 318–420

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	3d0f
Deposition date deposition_date	2008-05-01
Structure title title	Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718
Keywords keywords	;BIG_1156.2, penicillin-binding 1, Nitrosomonas europaea, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, Cell shape, Cell wall biogenesis/degradation, Glycosyltransferase, Peptidoglycan synthesis, Transferase, Transmembrane, UNKNOWN FUNCTION ;; 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.

3d0f__assembly_1__model_1

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

Download this curve (.dat)

3d0f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d0f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.58 Å
Rg (electron density)	19.98 Å
Total Rg	20.80 Å
Atom count	1639
Residues	208
Excluded volume	29311 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d0f__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 (4)

Entity 1 Entity 1 polymer

Description description	Penicillin-binding 1 transmembrane protein MrcA
Molecular weight formula_weight	11702.3 kDa
EC 编号 ec_number	2.4.2.-
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	2109

SNAYRGPEAFLKLPKDLKDREALQDIMQDIGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVKKTEKGSWQIVQLP

Source Source

Source organism organism	Nitrosomonas europaea ATCC 19718
NCBI taxonomy ID ncbi_taxonomy_id	228410
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	378

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3d0fA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3d0fB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	38.206 Å
Unit-cell length b length_b	52.219 Å
Unit-cell length c length_c	56.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.640 Å
Low-resolution limit resolution_low	35.670 Å
R factor r_factor	0.1730
R_work r_work	0.1700
R_free r_free	0.2170

Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718

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

Penicillin-binding 1 transmembrane protein MrcA

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

3d0f__assembly_1__model_1

3d0f__assembly_1__model_1 | I(q)

3d0f__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718

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

Penicillin-binding 1 transmembrane protein MrcA

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

3d0f__assembly_1__model_1

3d0f__assembly_1__model_1 | I(q)

3d0f__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)