SAXSdb — 6m7y

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

Nisin biosynthesis protein NisB

Lactococcus lactis subsp. lactis

UniProt P20103

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Lantibiotic × 1 （Q7BB86） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Lantibiotic × 1 （Q7BB86） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NISB_LACLL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–996； UniProt 2–993 Author chain B； PDBConstruct 5–996； UniProt 2–993

Lantibiotic

OrganismNot specified

UniProt Q7BB86

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nisin biosynthesis protein NisB × 1 （P20103） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Nisin biosynthesis protein NisB × 1 （P20103） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7BB86_9LACT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–34； UniProt 2–35 Author chain D； PDBConstruct 1–34； UniProt 2–35

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	6m7y
Deposition date deposition_date	2018-08-21
Structure title title	Dehydratase, NisB, bound to a non-eliminable substrate analog
Keywords keywords	RiPP, nisin, tRNA-dependent, dehydratase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

6m7y__assembly_1__model_1

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

Download this curve (.dat)

6m7y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6m7y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.12 Å
Rg (electron density)	34.82 Å
Total Rg	35.41 Å
Atom count	8065
Residues	954
Excluded volume	144880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6m7y__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6m7y__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Nisin biosynthesis protein NisB
Molecular weight formula_weight	118647.1 kDa
Mutation mutation	V169C
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	16392

GSHMIKSSFKAQPFLVRNTILCPNDKRSFTEYTQVIETVSKNKVFLEQLLLANPKLYDVMQKYNAGLLKKKRVKKLFESIYKYYKRSYLRSTPFGLFSETSIGVFSKSSQYKLMGKTTKGIRLDTQWLIRLVHKMEVDFSKKLSFTRNNANYKFGDRVFQVYTINSSELEECNIKYTNVYQIISEFCENDYQKYEDICETVTLCYGDEYRELSEQYLGSLIVNHYLISNLQKDLLSDFSWNTFLTKVEAIDEDKKYIIPLKKVQKFIQEYSEIEIGEGIEKLKEIYQEMSQILENDNYIQIDLISDSEINFDVKQKQQLEHLAEFLGNTTKSVRRTYLDDYKDKFIEKYGVDQEVQITELFDSTFGIGAPYNYNHPRNDFYESEPSTLYYSEEEREKYLSMYVEAVKNHNVINLDDLESHYQKMDLEKKSELQGLELFLNLAKEYEKDIFILGDIVGNNNLGGASGRFSALSPELTSYHRTIVDSVERENENKEITSCEIVFLPENIRHANVMHTSIMRRKVLPFFTSTSHNEVLLTNIYIGIDEKEKFYARDISTQEVLKFYITSMYNKTLFSNELRFLYEISLDDKFGNLPWELIYRDFDYIPRLVFDEIVISPAKWKIWGRDVNSKMTIRELIQSKEIPKEFYIVNGDNKVYLSQKNPLDMEILESAIKKSSKRKDFIELQEYFEDENIINKGEKGRVADVVVPFIRTRALGNEGRAFIREKRVSVERREKLPFNEWLYLKLYISINRQNEFLLSYLPDIQKIVANLGGNLFFLRYTDPKPHIRLRIKCSDLFLAYGSILEILKRSRKNRIMSTFDISIYDQEVERYGGFDTLELSEAIFCADSKIIPNLLTLIKDTNNDWKVDDVSILVNYLYLKCFFQNDNKKILNFLNLVSTKKVKENVNEKIEHYLKLLKVNNLGDQIFYDKNFKELKHAIKNLFLKMIAQDFELQKVYSIIDSIIHVHNNRLIGIERDKEKLIYYTLQRLFVSEEYMK

Source Source

Source organism organism	Lactococcus lactis subsp. lactis
NCBI taxonomy ID ncbi_taxonomy_id	1360
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Lantibiotic
Molecular weight formula_weight	3641.1 kDa
Mutation mutation	S12C, S26(J9A), C30A, C34A
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

STKDFNLDLVCVSKKDSGASPRITXISLATPGAK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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Unit-cell length a length_a	99.644 Å
Unit-cell length b length_b	107.143 Å
Unit-cell length c length_c	135.438 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.57 °
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	2.794 Å
Low-resolution limit resolution_low	29.393 Å
R factor r_factor	0.1890
R_work r_work	0.1849
R_free r_free	0.2696

Dehydratase, NisB, bound to a non-eliminable substrate analog

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

Nisin biosynthesis protein NisB

State in the Current Structure

Other States of the Same Protein in the Database

Lantibiotic

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

6m7y__assembly_1__model_1

6m7y__assembly_1__model_1 | I(q)

6m7y__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)

Dehydratase, NisB, bound to a non-eliminable substrate analog

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

Nisin biosynthesis protein NisB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lantibiotic

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

6m7y__assembly_1__model_1

6m7y__assembly_1__model_1 | I(q)

6m7y__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)