SAXSdb — 3e0r

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

C3-degrading proteinase (CppA protein)

Streptococcus pneumoniae

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	CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	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	Q9X4I9_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–244； UniProt 1–241 Author chain B； PDBConstruct 4–244； UniProt 1–241 Author chain C； PDBConstruct 4–244； UniProt 1–241 Author chain D； PDBConstruct 4–244； UniProt 1–241

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	3e0r
Deposition date deposition_date	2008-07-31
Structure title title	Crystal structure of cppA protein from Streptococcus pneumoniae TIGR4
Keywords keywords	;cppA, C3-degrading proteinase, MCSG, PSI, SAD, Structural Genomics, Protein Structure Initiative, Midwest Center for Structural Genomics, 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.

3e0r__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3e0r__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e0r__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	19.30 Å
Rg (electron density)	18.04 Å
Total Rg	18.97 Å
Atom count	1878
Residues	230
Excluded volume	33821 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e0r__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3e0r__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3e0r__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3e0r__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	C3-degrading proteinase (CppA protein)
Molecular weight formula_weight	27984.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8192

SNAMNVNQIVRIIPTLKANNRKLNETFYIETLGMKALLEESAFLSLGDQTGLEKLVLEEAPSMRTRKVEGRKKLARLIVKVENPLEIEGILSKTDSIHRLYKGQNGYAFEIFSPEDDLILIHAEDDIASLVEVGEKPEFQTDLASISLSKFEISMELHLPTDIESFLESSEIGASLDFIPAQGQDLTVDNTVTWDLSMLKFLVNELDIASLRQKFESTEYFIPKSEKFFLGKDRNNVELWFEEV

Source Source

Source organism organism	Streptococcus pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	1313
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	549

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3e0rA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	3e0rA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	40 — C3-degrading proteinase like domains

Domain ID domain_id	3e0rB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	3e0rB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	40 — C3-degrading proteinase like domains

Domain ID domain_id	3e0rC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	3e0rC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	40 — C3-degrading proteinase like domains

Domain ID domain_id	3e0rD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	3e0rD02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	40 — C3-degrading proteinase like domains

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Unit-cell length a length_a	114.742 Å
Unit-cell length b length_b	130.741 Å
Unit-cell length c length_c	91.535 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1928
R_work r_work	0.1893
R_free r_free	0.2563

Crystal structure of cppA protein from Streptococcus pneumoniae TIGR4

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

C3-degrading proteinase (CppA protein)

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

3e0r__assembly_4__model_1

3e0r__assembly_4__model_1 | I(q)

3e0r__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of cppA protein from Streptococcus pneumoniae TIGR4

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

C3-degrading proteinase (CppA protein)

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

3e0r__assembly_4__model_1

3e0r__assembly_4__model_1 | I(q)

3e0r__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)