← Back to search
1yl7

the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)

Method: X-RAY DIFFRACTION Dmax: 174.3 Å Quality: GOOD
▼

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 Chain C； UniProt 2–245 Chain D； UniProt 2–245 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
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 2–245 Chain F； UniProt 2–245 Chain G； UniProt 2–245 Chain H； UniProt 2–245 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

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 1YL7 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 mutation/modification 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 mutation/modification 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
1YL5 Crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (RV2773C) (crystal form A) 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）
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
1YL6 crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B) 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）
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

4 other PDB entries and 4 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 2–245； UniProt 2–245 Author chain B； PDBConstruct 2–245； UniProt 2–245 Author chain C； PDBConstruct 2–245； UniProt 2–245 Author chain D； PDBConstruct 2–245； UniProt 2–245 Author chain E； PDBConstruct 2–245； UniProt 2–245 Author chain F； PDBConstruct 2–245； UniProt 2–245 Author chain G； PDBConstruct 2–245； UniProt 2–245 Author chain H； PDBConstruct 2–245； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 1yl7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yl7
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1yl7
Deposition date deposition_date2005-01-19
Structure title titlethe crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)
Keywords keywords;lysine biosynthesis, dihydrodipicolinate, reductase, NADH, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier50.65 Å
Radius of gyration Rg (electron density) rg_electron50.80 Å
Forward intensity I(0) i0650433000.00
Molecular weight molecular_weight209960.0 kDa
Excluded volume excluded_volume262290 ų
Envelope volume envelope_volume368110 ų
Hydration-shell volume shell_volume62598 ų
Envelope diameter envelope_diameter182.3 Å
Shell Rg shell_rg51.84 Å
Envelope Rg envelope_rg49.61 Å
Shape Rg shape_rg50.79 Å
Total Rg total_rg50.84 Å
Total atoms total_atoms14786
Residues n_residues1960
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax174.3 Å
Rg (real space) rg_real50.89 Å
Rg uncertainty (real space) rg_real_error2.00 Å
I(0) (real space) i0_real6.5040e+08
I(0) uncertainty (real space) i0_real_error1.2400e+07
Rg (reciprocal space) rg_reciprocal50.44 Å
I(0) (reciprocal space) i0_reciprocal650000000.0000
Solution quality estimate total_estimate0.8441
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.0 Å
Skewness Skewness skewness0.425
Kurtosis Kurtosis kurtosis-0.497
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48910000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.798; Smooth: 0.812
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (24 domains)

Domain ID domain_idd1yl7a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yl7b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7b3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yl7c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7c3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yl7d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yl7e1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7e2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7e3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yl7f1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7f2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7f3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yl7g1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7g2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7g3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1yl7h1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1yl7h2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.3 — Dihydrodipicolinate reductase-like
Domain ID domain_idd1yl7h3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (16 domains)

Domain ID domain_id1yl7A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1yl7B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1yl7C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7C02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1yl7D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7D02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1yl7E01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7E02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1yl7F01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7F02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1yl7G01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7G02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1yl7H01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1yl7H02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
▶

8. Citations (1)

▶

9. Files and Curves (10)