SAXSdb — 4a8d

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

PERIPLASMIC SERINE ENDOPROTEASE DEGP

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	OUTER MEMBRANE PROTEIN C × 1 （P06996）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEGP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–448； UniProt 27–474 Author chain B； PDBConstruct 1–448； UniProt 27–474 Author chain C； PDBConstruct 1–448； UniProt 27–474 Author chain D； PDBConstruct 1–448； UniProt 27–474 Author chain E； PDBConstruct 1–448； UniProt 27–474 Author chain F； PDBConstruct 1–448； UniProt 27–474 Author chain G； PDBConstruct 1–448； UniProt 27–474 Author chain H； PDBConstruct 1–448； UniProt 27–474 Author chain I； PDBConstruct 1–448； UniProt 27–474 Author chain J； PDBConstruct 1–448； UniProt 27–474 Author chain K； PDBConstruct 1–448； UniProt 27–474 Author chain L； PDBConstruct 1–448； UniProt 27–474

OUTER MEMBRANE PROTEIN C

OrganismNot specified

UniProt P06996

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	PERIPLASMIC SERINE ENDOPROTEASE DEGP × 12 （P0C0V0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OMPC_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–345； UniProt 22–367

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	4a8d
Deposition date deposition_date	2011-11-20
Structure title title	DegP dodecamer with bound OMP
Keywords keywords	HYDROLASE-TRANSPORT PROTEIN COMPLEX, CHAPERONE; HYDROLASE/TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

4a8d__assembly_1__model_1

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

Download this curve (.dat)

4a8d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4a8d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	59.50 Å
Rg (electron density)	58.92 Å
Total Rg	59.02 Å
Atom count	0
Residues	0
Excluded volume	638670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4a8d__assembly_1__model_1`	tridecameric （13）	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	PERIPLASMIC SERINE ENDOPROTEASE DEGP
Molecular weight formula_weight	46852.9 kDa
EC 编号 ec_number	3.4.21.107
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	4954

AETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLMQ

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	OUTER MEMBRANE PROTEIN C
Molecular weight formula_weight	38336.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

AEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	28.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	28.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	6285

DegP dodecamer with bound OMP

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

PERIPLASMIC SERINE ENDOPROTEASE DEGP

State in the Current Structure

Other States of the Same Protein in the Database

OUTER MEMBRANE PROTEIN C

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

4a8d__assembly_1__model_1

4a8d__assembly_1__model_1 | I(q)

4a8d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Citations (2)

DegP dodecamer with bound OMP

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

PERIPLASMIC SERINE ENDOPROTEASE DEGP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

OUTER MEMBRANE PROTEIN C

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

4a8d__assembly_1__model_1

4a8d__assembly_1__model_1 | I(q)

4a8d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Citations (2)