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5loc

Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH)

Method: X-RAY DIFFRACTION Dmax: 92.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Meso-diaminopimelate D-dehydrogenase

Corynebacterium glutamicum

UniProt P04964

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 2–320 Chain B； UniProt 2–320 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.12 M monosaccharides, 0.1 M Buffer System 3 pH 8.5, 30%, P500MME_P20K Resolution 2.04 Å R-free 0.255

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 5LOC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DAP C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ Deposited 1996-07-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–320（320 aa）
Chain B 1–320（320 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；13-17% PEG 8000 IN 100 MM NA-CACODYLATE, PH 6.5, 150-300 MM MG-ACETATE CRYSTAL
Resolution 2.20 Å
1F06 THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE Deposited 2000-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–320（320 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 8000, magnesium acetate, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.209
1F06 THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE Deposited 2000-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–320（320 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 2NP L-2-AMINO-6-METHYLENE-PIMELIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 8000, magnesium acetate, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.209
1F06 THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE Deposited 2000-05-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–320（320 aa）
Chain B 1–320（320 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 2NP L-2-AMINO-6-METHYLENE-PIMELIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG 8000, magnesium acetate, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.209
2DAP C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP Deposited 1997-12-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–320（320 aa）
Not recorded API 2,6-DIAMINOPIMELIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；13-17% PEG 8000 IN 100 MM NA-CACODYLATE, PH 6.5, 150-300 MM MG-ACETATE CRYSTAL
Resolution 2.20 Å R-free 0.258
3DAP C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE Deposited 1997-12-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–320（320 aa）
Chain B 1–320（320 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 DA3 (2S,5',S)-2-AMINO-3-(3-CARBOXY-2-ISOXAZOLIN-5-YL)PROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；13-17% PEG 8000 IN 100 MM NA-CACODYLATE, PH 6.5, 150-300 MM MG-ACETATE CRYSTAL
Resolution 2.20 Å R-free 0.233
5LOA Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH) bound to NADP+ Deposited 2016-08-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–320（319 aa）
Chain B 2–320（319 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2 M sodium formate, 0.1 M Bis-Tris propane pH 8.5 and 20% PEG 3350
Resolution 1.84 Å R-free 0.206

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

View Construct and Data Evidence
UniProt name DAPDH_CORGL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–320； UniProt 2–320 Author chain B； PDBConstruct 2–320； UniProt 2–320

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 5loc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5loc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5loc
Deposition date deposition_date2016-08-09
Structure title titleCrystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH)
Keywords keywordsDAADH, biocatalysis, amino acids, asymmetric synthesis, enzyme catalysis, oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.18 Å
Radius of gyration Rg (electron density) rg_electron27.28 Å
Forward intensity I(0) i084101700.00
Molecular weight molecular_weight69696.0 kDa
Excluded volume excluded_volume86228 ų
Envelope volume envelope_volume108680 ų
Hydration-shell volume shell_volume33589 ų
Envelope diameter envelope_diameter96.7 Å
Shell Rg shell_rg34.30 Å
Envelope Rg envelope_rg27.50 Å
Shape Rg shape_rg27.27 Å
Total Rg total_rg27.97 Å
Total atoms total_atoms4909
Residues n_residues637
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.6 Å
Rg (real space) rg_real28.14 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real8.4100e+07
I(0) uncertainty (real space) i0_real_error1.3520e+06
Rg (reciprocal space) rg_reciprocal28.16 Å
I(0) (reciprocal space) i0_reciprocal84100000.0000
Solution quality estimate total_estimate0.8879
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.1 Å
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.285
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15070000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.950
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5locA01
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_id5locA02
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_id5locB01
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_id5locB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
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8. Citations (1)

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9. Files and Curves (10)