SAXSdb — 1f06

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

MESO-DIAMINOPIMELATE D-DEHYDROGENASE

Corynebacterium glutamicum

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–320	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–320	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–320 Chain B； UniProt 1–320	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

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 1F06	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 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
2DAP C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP Deposited 1997-12-23	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 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 construct 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
5LOC Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH) Deposited 2016-08-09	Different construct 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	No recorded non-water small molecule	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

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

View Construct and Data Evidence

UniProt name	DDH_CORGL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–320； UniProt 1–320 Author chain B； PDBConstruct 1–320； UniProt 1–320

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1f06
Deposition date deposition_date	2000-05-14
Structure title title	THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE
Keywords keywords	Enzyme-NADPH-inhibitor ternary complex, 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	27.71 Å
Radius of gyration Rg (electron density) rg_electron	26.83 Å
Forward intensity I(0) i0	92774000.00
Molecular weight molecular_weight	71924.0 kDa
Excluded volume excluded_volume	88315 Å³
Envelope volume envelope_volume	106040 Å³
Hydration-shell volume shell_volume	33203 Å³
Envelope diameter envelope_diameter	94.0 Å
Shell Rg shell_rg	33.97 Å
Envelope Rg envelope_rg	27.07 Å
Shape Rg shape_rg	26.83 Å
Total Rg total_rg	27.51 Å
Total atoms total_atoms	5059
Residues n_residues	640
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	88.6 Å
Rg (real space) rg_real	27.70 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	9.2770e+07
I(0) uncertainty (real space) i0_real_error	1.4070e+06
Rg (reciprocal space) rg_reciprocal	27.70 Å
I(0) (reciprocal space) i0_reciprocal	92770000.0000
Solution quality estimate total_estimate	0.8933
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.363
Kurtosis Kurtosis kurtosis	-0.311
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17910000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.894

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	MESO-DIAMINOPIMELATE D-DEHYDROGENASE
Molecular weight formula_weight	35242.3 kDa
EC 编号 ec_number	1.4.1.16
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	5175

MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVADVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQGHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVVADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLLSPENLDDLIARDV

来源 Source

来源生物 organism	Corynebacterium glutamicum
NCBI Class编号 ncbi_taxonomy_id	1718
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	L-2-AMINO-6-METHYLENE-PIMELIC ACID
Molecular weight formula_weight	187.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1f06a1
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	d1f06a2
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	d1f06b1
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	d1f06b2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1f06A01
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	1f06A02
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	1f06B01
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	1f06B02
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	75.547 Å
Unit-cell length b length_b	65.591 Å
Unit-cell length c length_c	84.281 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.52 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	48.600 Å
R factor r_factor	0.1850
R_work r_work	0.1790
R_free r_free	0.2090

fit	/app/data/saxs_computation/f0/1f06/1f06.fit
pddf	/app/data/pr_computation/f0/1f06/1f06.pr.out
profile	/app/data/saxs_computation/f0/1f06/1f06.dat

THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE

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

MESO-DIAMINOPIMELATE D-DEHYDROGENASE

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