SAXSdb — 2ntf

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

Murine Antibody Fab RS2-1G9 Lambda Light Chain

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 20–230	Not recorded	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain × 1 （Q99LC4） OHM 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00	Resolution 3.18 Å R-free 0.265
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 20–230	Not recorded	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain × 1 （Q99LC4） OHM 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00	Resolution 3.18 Å R-free 0.265
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 20–230 Chain L； UniProt 20–230	Not recorded	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain × 2 （Q99LC4） OHM 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00	Resolution 3.18 Å R-free 0.265

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q0VDX6_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 20–230 Author chain L； PDBConstruct 1–211； UniProt 20–230

Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain

OrganismNot specified

UniProt Q99LC4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 20–239	Not recorded	Murine Antibody Fab RS2-1G9 Lambda Light Chain × 1 （Q0VDX6） OHM 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00	Resolution 3.18 Å R-free 0.265
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 20–239	Not recorded	Murine Antibody Fab RS2-1G9 Lambda Light Chain × 1 （Q0VDX6） OHM 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00	Resolution 3.18 Å R-free 0.265
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 20–239 Chain H； UniProt 20–239	Not recorded	Murine Antibody Fab RS2-1G9 Lambda Light Chain × 2 （Q0VDX6） OHM 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；1.0M Na/K Tartrate, 0.2M NaCl, 0.1 Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 8.00	Resolution 3.18 Å R-free 0.265

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2NTF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AFV HIV-1 CAPSID PROTEIN (P24) COMPLEX WITH FAB25.3 Deposited 1997-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 20–238（219 aa） Fragment：LIGHT CHAIN RESIDUES 1 - 217, HEAVY CHAIN RESIDUES 1 - 220 Chain K 20–238（219 aa） Fragment：LIGHT CHAIN RESIDUES 1 - 217, HEAVY CHAIN RESIDUES 1 - 220	Not recorded	PB LEAD (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；16% PEG 3350, 50 MM BISTRIS-HCL, PH 7.0, 0.1% BETA-OCTYLGLUCOSIDE, 1 MM NAN3	Resolution 3.70 Å R-free 0.324
3HKF Murine unglycosylated IgG Fc fragment Deposited 2009-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 252–463（212 aa） Fragment：UNP residues 252-463	Not recorded	MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；2-ethoxyethanol, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.305
5MP3 Crystal structure of DC8E8 Fab in the complex with a 30-mer tau peptide at pH 6.5 Deposited 2016-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 21–239（219 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG 8000, 0.1 M Na-cacodylate, 0.2 M Mg-acetate	Resolution 2.75 Å R-free 0.249
5MP3 Crystal structure of DC8E8 Fab in the complex with a 30-mer tau peptide at pH 6.5 Deposited 2016-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 21–239（219 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG 8000, 0.1 M Na-cacodylate, 0.2 M Mg-acetate	Resolution 2.75 Å R-free 0.249
6C5H S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen Deposited 2018-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 126–239（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289.15 K；0.1 M BIS-Tris HCl 25% [w/v] polyethylene glycol [PEG] 3350	Resolution 1.99 Å R-free 0.226
6C5I Unliganded S25-5 Fab Deposited 2018-01-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 126–239（114 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 1 NI NICKEL (II) ION × 2 PG0 2-(2-METHOXYETHOXY)ETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289.15 K；0.01 M NiCl2, 0.1 M Tris-HCl, 20% [w/v] PEG 2000 MME	Resolution 1.89 Å R-free 0.231
6C5J S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1) Deposited 2018-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 126–239（114 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289.15 K；0.1 M MES, 20% [w/v] polyethylene glycol [PEG] 10000	Resolution 2.29 Å R-free 0.239
6C5K S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2) Deposited 2018-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 126–239（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Potassium nitrate, 20% [w/v] polyethylene glycol 3350	Resolution 1.75 Å R-free 0.218
6C5K S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2) Deposited 2018-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 126–239（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Potassium nitrate, 20% [w/v] polyethylene glycol 3350	Resolution 1.75 Å R-free 0.218

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q99LC4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–222； UniProt 20–239 Author chain H； PDBConstruct 1–222； UniProt 20–239

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	2ntf
Deposition date deposition_date	2006-11-07
Structure title title	Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog
Keywords keywords	Immunoglobulin, antibody, Fab, hapten complex, quorum sensing, homoserine lactone, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.89 Å
Radius of gyration Rg (electron density) rg_electron	29.97 Å
Forward intensity I(0) i0	142557000.00
Molecular weight molecular_weight	94330.0 kDa
Excluded volume excluded_volume	117770 Å³
Envelope volume envelope_volume	150990 Å³
Hydration-shell volume shell_volume	41508 Å³
Envelope diameter envelope_diameter	110.4 Å
Shell Rg shell_rg	37.76 Å
Envelope Rg envelope_rg	29.57 Å
Shape Rg shape_rg	29.94 Å
Total Rg total_rg	30.77 Å
Total atoms total_atoms	6652
Residues n_residues	840
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	103.8 Å
Rg (real space) rg_real	30.76 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.4260e+08
I(0) uncertainty (real space) i0_real_error	1.9190e+06
Rg (reciprocal space) rg_reciprocal	30.82 Å
I(0) (reciprocal space) i0_reciprocal	142600000.0000
Solution quality estimate total_estimate	0.8779
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.7 Å
Skewness Skewness skewness	0.230
Kurtosis Kurtosis kurtosis	-0.252
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25850000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Murine Antibody Fab RS2-1G9 Lambda Light Chain
Molecular weight formula_weight	22840.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,A
Atom count atom_count	6652

QAVVTQESALTTSPGETVTLTCRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGVPARFSGSLIGHKAALTITGAQTEDESVYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTAGAWERHSSYSCQVTHEGHTVEKSLSR

Entity 2 Entity 2 polymer

Description description	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain
Molecular weight formula_weight	24082.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,B

QVQLQQSGSELVRPGASVKLSCKASGYTFTTYWIHWVKQRPGQGLEWIGTIYPGSDNTYYDEKFKNKATLTVDTSSSTAFMQLSSLTSEDSAVYFCTRGSLYYNNYGWFGYWGQGTLVTVSAAKTTPPSVYPLAPGSNAASQSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR

Entity 3 Entity 3 non-polymer

Description description	3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE
Molecular weight formula_weight	296.4 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2ntfa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfa2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2ntfb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id	2ntfA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	118.659 Å
Unit-cell length b length_b	118.659 Å
Unit-cell length c length_c	176.042 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.180 Å
Low-resolution limit resolution_low	44.020 Å
R factor r_factor	0.2130
R_work r_work	0.2100
R_free r_free	0.2650

fit	/app/data/saxs_computation/nt/2ntf/2ntf.fit
pddf	/app/data/pr_computation/nt/2ntf/2ntf.pr.out
profile	/app/data/saxs_computation/nt/2ntf/2ntf.dat

Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog

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

Murine Antibody Fab RS2-1G9 Lambda Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)