SAXSdb — 1yl5

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

Dihydrodipicolinate reductase

Mycobacterium tuberculosis

UniProt P72024

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–245 Chain B； UniProt 2–245	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris/HCl, 20 % PEG 3350, 120 mM MgCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.30 Å R-free 0.249

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 1YL5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C3V DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND PDC Deposited 1999-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–245（245 aa） Chain B 1–245（245 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 PDC PYRIDINE-2,6-DICARBOXYLIC ACID × 4 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K	Resolution 2.39 Å R-free 0.243
1P9L Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 PDC Deposited 2003-05-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–245（245 aa） Chain B 1–245（245 aa）	Not recorded	NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 PDC PYRIDINE-2,6-DICARBOXYLIC ACID × 4 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium Sulfate, PEG 400, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.250
1YL6 crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B) Deposited 2005-01-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–245（244 aa） Chain B 2–245（244 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris/HCl, 24 % PEG 3350, 140 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.90 Å R-free 0.257
1YL7 the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C) Deposited 2005-01-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–245（244 aa） Chain B 2–245（244 aa） Chain C 2–245（244 aa） Chain D 2–245（244 aa）	Not recorded	MG MAGNESIUM ION × 3 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris/HCl, 26 % PEG 3350, 140 mM MgCl2 + 3 mM NADH in the protein solution, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.34 Å R-free 0.238
1YL7 the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C) Deposited 2005-01-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 2–245（244 aa） Chain F 2–245（244 aa） Chain G 2–245（244 aa） Chain H 2–245（244 aa）	Not recorded	MG MAGNESIUM ION × 3 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；100 mM Tris/HCl, 26 % PEG 3350, 140 mM MgCl2 + 3 mM NADH in the protein solution, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.34 Å R-free 0.238

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DAPB_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–247； UniProt 2–245 Author chain B； PDBConstruct 4–247； UniProt 2–245

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	1yl5
Deposition date deposition_date	2005-01-19
Structure title title	Crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A)
Keywords keywords	;lysine biosynthesis, dihydrodipicolinate, reductase, NADH, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, OXIDOREDUCTASE ;; 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	26.93 Å
Radius of gyration Rg (electron density) rg_electron	26.06 Å
Forward intensity I(0) i0	44744500.00
Molecular weight molecular_weight	51782.0 kDa
Excluded volume excluded_volume	65000 Å³
Envelope volume envelope_volume	81074 Å³
Hydration-shell volume shell_volume	26859 Å³
Envelope diameter envelope_diameter	89.5 Å
Shell Rg shell_rg	32.33 Å
Envelope Rg envelope_rg	26.02 Å
Shape Rg shape_rg	26.04 Å
Total Rg total_rg	26.84 Å
Total atoms total_atoms	3650
Residues n_residues	492
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	86.8 Å
Rg (real space) rg_real	26.94 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	4.4740e+07
I(0) uncertainty (real space) i0_real_error	6.6500e+05
Rg (reciprocal space) rg_reciprocal	26.94 Å
I(0) (reciprocal space) i0_reciprocal	44740000.0000
Solution quality estimate total_estimate	0.6914
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.449
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6037000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 0.089; Positv: 1.000; Valcen: 0.970; Smooth: 0.978

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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	Dihydrodipicolinate reductase
Molecular weight formula_weight	25905.5 kDa
EC 编号 ec_number	1.3.1.26
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	3699

AMARVGVLGAKGKVGATMVRAVAAADDLTLSAELDAGDPLSLLTDGNTEVVIDFTHPDVVMGNLEFLIDNGIHAVVGTTGFTAERFQQVESWLVAKPNTSVLIAPNFAIGAVLSMHFAKQAARFFDSAEVIELHHPHKADAPSGTAARTAKLIAEARKGLPPNPDATSTSLPGARGADVDGIPVHAVRLAGLVAHQEVLFGTEGETLTIRHDSLDRTSFVPGVLLAVRRIAERPGLTVGLEPLLDLH

来源 Source

来源生物 organism	Mycobacterium tuberculosis
NCBI Class编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1yl5a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1yl5a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

Domain ID domain_id	d1yl5a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1yl5b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1yl5b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

Domain ID domain_id	d1yl5b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1yl5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1yl5A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1yl5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1yl5B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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8. Citations (1)

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Unit-cell length a length_a	59.260 Å
Unit-cell length b length_b	122.000 Å
Unit-cell length c length_c	77.930 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2070
R_work r_work	0.2051
R_free r_free	0.2492

fit	/app/data/saxs_computation/yl/1yl5/1yl5.fit
pddf	/app/data/pr_computation/yl/1yl5/1yl5.pr.out
profile	/app/data/saxs_computation/yl/1yl5/1yl5.dat

Crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A)

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

Dihydrodipicolinate reductase

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