SAXSdb — 4wvi

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

Maltose-binding periplasmic protein,Signal peptidase IB

Staphylococcus aureus subsp. aureus str. Newman

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 其他Polymer 1	substrate peptide (pep2) × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–372； UniProt 33–392

Maltose-binding periplasmic protein,Signal peptidase IB

Staphylococcus aureus subsp. aureus str. Newman

UniProt Q5HHB9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 其他Polymer 1	substrate peptide (pep2) × 1 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEP_STAAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 377–526； UniProt 26–175

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	4wvi
Deposition date deposition_date	2014-11-05
Structure title title	Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep2).
Keywords keywords	SpsB Type-I signal peptidase, Peptide complex, Cell secretion, MBP fusion, 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.

4wvi__assembly_1__model_1

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

Download this curve (.dat)

4wvi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wvi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.31 Å
Rg (electron density)	27.61 Å
Total Rg	28.25 Å
Atom count	4097
Residues	531
Excluded volume	72905 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wvi__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	Maltose-binding periplasmic protein,Signal peptidase IB
Molecular weight formula_weight	59189.8 kDa
EC 编号 ec_number	3.4.21.89
Mutation mutation	K143G, Q78C, R393N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4477

MSYYHHHHHHHMLVIWINGDKGYNGLAQVGKKFEKDTGIKVTVEHPYKLEEKFPQVAATGDGPDIIFWAHDRFGGYACSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDGELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAGAIVTPYTIKGESMDPTLKDGERVAVNIVGYKTGGLEKGNVVVFHANKNDDYVKRVIGVPGDKVEYKNDTLYVNGKKQDEPYLNYNLKHKQGDYITGTFQVKDLPNANPKSNVIPKGKYLVLGDNREVSKDSRAFGLIDEDQIVGKVSFRFWSHPQFEK

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus str. Newman
NCBI taxonomy ID ncbi_taxonomy_id	426430
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	substrate peptide (pep2)
Molecular weight formula_weight	886.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GGGGAVPTAKA

Entity 3 Entity 3 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
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	371

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Unit-cell length a length_a	63.989 Å
Unit-cell length b length_b	80.232 Å
Unit-cell length c length_c	119.879 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	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.780 Å
R factor r_factor	0.1895
R_work r_work	0.1879
R_free r_free	0.2194

Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep2).

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

Maltose-binding periplasmic protein,Signal peptidase IB

State in the Current Structure

Other States of the Same Protein in the Database

Maltose-binding periplasmic protein,Signal peptidase IB

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

4wvi__assembly_1__model_1

4wvi__assembly_1__model_1 | I(q)

4wvi__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 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep2).

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

Maltose-binding periplasmic protein,Signal peptidase IB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Maltose-binding periplasmic protein,Signal peptidase IB

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

4wvi__assembly_1__model_1

4wvi__assembly_1__model_1 | I(q)

4wvi__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 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

7. Citations (1)