SAXSdb — 1ojt

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

SURFACE PROTEIN

Neisseria meningitidis

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 112–593	Fragment：DIHYDROLIPOAMIDE DEHYDROGENASE DOMAIN	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；BRIGHT YELLOW CRYSTALS WERE GROWN IN 24-WELL LINBRO PLATES USING HANGING DROP DIFFUSION METHOD AT ROOM TEMPERATURE. RESERVOIR: 1 ML CONTAINING 0.1M POTASSIUM PHOSPHATE AND 2M AMMONIUM SULFATE (PH 7.0). PRISM CRYSTALS TYPICALLY IN TWO WEEKS AT ROOM TEMPERATURE., vapor diffusion - hanging drop THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDES A FAD COFACTOR BUT NOT THE NADH. THE E3 DOMAIN (117-601) CRYSTALLIZES IN AMMONIUM SULFATE. IT INCLUDE A FAD COFACTOR BUT NOT THE NADH.	Resolution 2.75 Å R-free 0.232

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 1OJT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BHY LOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF P64K FROM MASC DATA Deposited 1998-06-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 112–593（482 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULPHATE	Resolution 4.18 Å R-free 0.323

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q51225_NEIME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–482； UniProt 112–593

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	1ojt
Deposition date deposition_date	1996-09-06
Structure title title	STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE
Keywords keywords	REDOX-ACTIVE CENTER, GLYCOLYSIS, OXIDOREDUCTASE, NAD, FLAVOPROTEIN, FAD, P64K; OXIDOREDUCTASE
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	24.99 Å
Radius of gyration Rg (electron density) rg_electron	24.03 Å
Forward intensity I(0) i0	45035400.00
Molecular weight molecular_weight	51436.0 kDa
Excluded volume excluded_volume	64260 Å³
Envelope volume envelope_volume	77523 Å³
Hydration-shell volume shell_volume	26795 Å³
Envelope diameter envelope_diameter	88.0 Å
Shell Rg shell_rg	31.20 Å
Envelope Rg envelope_rg	24.14 Å
Shape Rg shape_rg	24.04 Å
Total Rg total_rg	24.82 Å
Total atoms total_atoms	3609
Residues n_residues	482
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	86.5 Å
Rg (real space) rg_real	24.87 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	4.5040e+07
I(0) uncertainty (real space) i0_real_error	6.5630e+05
Rg (reciprocal space) rg_reciprocal	24.90 Å
I(0) (reciprocal space) i0_reciprocal	45040000.0000
Solution quality estimate total_estimate	0.7963
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.159
Kurtosis Kurtosis kurtosis	-0.563
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9195000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000

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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	SURFACE PROTEIN
Molecular weight formula_weight	50738.0 kDa
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	3724

GSADAEYDVVVLGGGPGGYSAAFAAADEGLKVAIVERYKTLGGVCLNVGCIPSKALLHNAAVIDEVRHLAANGIKYPEPELDIDMLRAYKDGVVSRLTGGLAGMAKSRKVDVIQGDGQFLDPHHLEVSLTAGDAYEQAAPTGEKKIVAFKNCIIAAGSRVTKLPFIPEDPRIIDSSGALALKEVPGKLLIIGGGIIGLEMGTVYSTLGSRLDVVEMMDGLMQGADRDLVKVWQKQNEYRFDNIMVNTKTVAVEPKEDGVYVTFEGANAPKEPQRYDAVLVAAGRAPNGKLISAEKAGVAVTDRGFIEVDKQMRTNVPHIYAIGDIVGQPMLAHKAVHEGHVAAENCAGHKAYFDARVIPGVAYTSPEVAWVGETELSAKASARKITKANFPWAASGRAIANGCDKPFTKLIFDAETGRIIGGGIVGPNGGDMIGEVCLAIEMGCDAADIGKTIHPHPTLGESIGMAAEVALGTCTDLPPQKK

来源 Source

来源生物 organism	Neisseria meningitidis
NCBI Class编号 ncbi_taxonomy_id	487
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 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	115

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ojta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1ojta2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.5 — FAD/NAD-linked reductases, N-terminal and central domains

Domain ID domain_id	d1ojta3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.87 — CO dehydrogenase flavoprotein C-domain-like
Superfamily Superfamily superfamily	d.87.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain
Family Family family	d.87.1.1 — FAD/NAD-linked reductases, dimerisation (C-terminal) domain

CATH v4.4 (3 domains)

Domain ID domain_id	1ojtA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1ojtA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1ojtA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

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8. Citations (4)

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Unit-cell length a length_a	138.050 Å
Unit-cell length b length_b	138.050 Å
Unit-cell length c length_c	79.770 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	8

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

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	18.000 Å
R factor r_factor	0.1730
R_work r_work	—
R_free r_free	0.2320

fit	/app/data/saxs_computation/oj/1ojt/1ojt.fit
pddf	/app/data/pr_computation/oj/1ojt/1ojt.pr.out
profile	/app/data/saxs_computation/oj/1ojt/1ojt.dat

STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE

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

SURFACE PROTEIN

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