SAXSdb — 8xud

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

Lipoprotein NlpI

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Tail-specific protease × 2 （P23865） Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase × 4 （P0AFV4） Substrate peptide × 1 Substrate peptide × 1 PHOSPHATE ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NLPI_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–297； UniProt 20–294 Author chain B； PDBConstruct 23–297； UniProt 20–294

Tail-specific protease

Escherichia coli K-12

UniProt P23865

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Lipoprotein NlpI × 2 （P0AFB1） Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase × 4 （P0AFV4） Substrate peptide × 1 Substrate peptide × 1 PHOSPHATE ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRC_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–682； UniProt 1–682 Author chain D； PDBConstruct 1–682； UniProt 1–682

Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase

Escherichia coli K-12

UniProt P0AFV4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	Lipoprotein NlpI × 2 （P0AFB1） Tail-specific protease × 2 （P23865） Substrate peptide × 1 Substrate peptide × 1 PHOSPHATE ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MEPS_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 2–162； UniProt 28–188 Author chain J； PDBConstruct 2–162； UniProt 28–188 Author chain K； PDBConstruct 2–162； UniProt 28–188 Author chain L； PDBConstruct 2–162； UniProt 28–188

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	8xud
Deposition date deposition_date	2024-01-12
Structure title title	Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc
Keywords keywords	hydrolases, lipoprotein, protease, protein complex, PROTEIN BINDING, SUBSTRATE DEGRADATION; PROTEIN BINDING
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.

8xud__assembly_1__model_1

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

Download this curve (.dat)

8xud__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8xud__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.48 Å
Rg (electron density)	51.92 Å
Total Rg	52.13 Å
Atom count	19377
Residues	2420
Excluded volume	341810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8xud__assembly_1__model_1`	decameric （10）	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 (6)

Entity 1 Entity 1 polymer

Description description	Lipoprotein NlpI
Molecular weight formula_weight	34082.7 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	19377

MGSSHHHHHHSSGENLYFQGHMSNTSWRKSEVLAVPLQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFVEHRYALLELSLLGQDQDDLAESDQQ

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Tail-specific protease
Molecular weight formula_weight	77520.8 kDa
EC 编号 ec_number	3.4.21.102
Mutation mutation	S452A/K477A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MNMFFRLTALAGLLAIAGQTFAVEDITRADQIPVLKEETQHATVSERVTSRFTRSHYRQFDLDQAFSAKIFDRYLNLLDYSHNVLLASDVEQFAKKKTELGDELRSGKLDVFYDLYNLAQKRRFERYQYALSVLEKPMDFTGNDTYNLDRSKAPWPKNEAELNALWDSKVKFDELSLKLTGKTDKEIRETLTRRYKFAIRRLAQTNSEDVFSLAMTAFAREIDPHTNYLSPRNTEQFNTEMSLSLEGIGAVLQMDDDYTVINSMVAGGPAAKSKAISVGDKIVGVGQTGKPMVDVIGWRLDDVVALIKGPKGSKVRLEILPAGKGTKTRTVTLTRERIRLEDRAVKMSVKTVGKEKVGVLDIPGFYVGLTDDVKVQLQKLEKQNVSSVIIDLRSNGGGALTEAVSLSGLFIPAGPIVQVRDNNGKVREDSDTDGQVFYKGPLVVLVDRFSAAASEIFAAAMQDYGRALVVGEPTFGAGTVQQYRSLNRIYDQMLRPEWPALGSVQYTIQKFYRVNGGSTQRKGVTPDIIMPTGNEETETGEKFEDNALPWDSIDAATYVKSGDLTAFEPELLKEHNARIAKDPEFQNIMKDIARFNAMKDKRNIVSLNYAVREKENNEDDATRLARLNERFKREGKPELKKLDDLPKDYQEPDPYLDETVNIALDLAKLEKARPAEQPAPVKHHHHHH

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
Molecular weight formula_weight	19148.4 kDa
EC 编号 ec_number	3.4.-.-,3.4.17.13
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L

MSANNTAKNMHPETRAVGSETSSLQASQDEFENLVRNVDVKSRIMDQYADWKGVRYRLGGSTKKGIDCSGFVQRTFREQFGLELPRSTYEQQEMGKSVSRSNLRTGDLVLFRAGSTGRHVGIYIGNNQFVHASTSSGVIISSMNEPYWKKRYNEARRVLSRSHHHHHH

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Substrate peptide
Molecular weight formula_weight	698.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

XXXXXXXX

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Substrate peptide
Molecular weight formula_weight	784.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

XXXXXXXXX

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	14

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Unit-cell length a length_a	230.410 Å
Unit-cell length b length_b	230.410 Å
Unit-cell length c length_c	182.905 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	tetragonal

Resolution resolution	3.490 Å
Low-resolution limit resolution_low	29.910 Å
R factor r_factor	0.2358
R_work r_work	0.2346
R_free r_free	0.2718

Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc

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

Lipoprotein NlpI

State in the Current Structure

Other States of the Same Protein in the Database

Tail-specific protease

State in the Current Structure

Other States of the Same Protein in the Database

Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase

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

8xud__assembly_1__model_1

8xud__assembly_1__model_1 | I(q)

8xud__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)

Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc

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

Lipoprotein NlpI

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tail-specific protease

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase

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

8xud__assembly_1__model_1

8xud__assembly_1__model_1 | I(q)

8xud__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)