SAXSdb — 1c1d

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

L-PHENYLALANINE DEHYDROGENASE

Rhodococcus sp.

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 2–356 Chain B； UniProt 2–356	Not recorded	K POTASSIUM ION × 4 PHE PHENYLALANINE × 2 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.7；pH 8.70	Resolution 1.25 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 1C1D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BW9 PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND PHENYLPYRUVATE Deposited 1998-10-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa） Chain B 1–356（356 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PPY 3-PHENYLPYRUVIC ACID × 2 K POTASSIUM ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 3 IPA ISOPROPYL ALCOHOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.7；pH 8.7	Resolution 1.50 Å
1BXG PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND BETA-PHENYLPROPIONATE Deposited 1998-10-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–356（356 aa） Chain B 1–356（356 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 HCI HYDROCINNAMIC ACID × 2 K POTASSIUM ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.7；pH 8.7	Resolution 2.30 Å
1C1X L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NAD+ AND L-3-PHENYLLACTATE Deposited 1999-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–356（355 aa） Chain B 2–356（355 aa）	Not recorded	K POTASSIUM ION × 4 NA SODIUM ION × 1 HFA ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PO4 PHOSPHATE ION × 1 IPA ISOPROPYL ALCOHOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions MACROSEEDED INTO BATCH；pH 8.7；296 K；1.2 M NA/K PHOSPHATE 50 MM CHES 2% ISOPROPANOL 5 MM NAD+ 10 MM L-3- PHENYLLACTATE 3.75 MG/ML PROTEIN, pH 8.7, MACROSEEDED INTO BATCH, temperature 296K	Resolution 1.40 Å R-free 0.229

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q59771_RHOSO
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 2–356 Author chain B； PDBConstruct 1–355； UniProt 2–356

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	1c1d
Deposition date deposition_date	1999-07-21
Structure title title	L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE
Keywords keywords	AMINO ACID DEHYDROGENASE, OXIDATIVE DEAMINATION MECHANISM, 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	36.09 Å
Radius of gyration Rg (electron density) rg_electron	36.01 Å
Forward intensity I(0) i0	90255200.00
Molecular weight molecular_weight	73560.0 kDa
Excluded volume excluded_volume	90708 Å³
Envelope volume envelope_volume	119290 Å³
Hydration-shell volume shell_volume	27590 Å³
Envelope diameter envelope_diameter	113.8 Å
Shell Rg shell_rg	42.34 Å
Envelope Rg envelope_rg	35.28 Å
Shape Rg shape_rg	36.00 Å
Total Rg total_rg	36.46 Å
Total atoms total_atoms	5151
Residues n_residues	697
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	117.3 Å
Rg (real space) rg_real	36.36 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	9.0260e+07
I(0) uncertainty (real space) i0_real_error	1.6160e+06
Rg (reciprocal space) rg_reciprocal	36.20 Å
I(0) (reciprocal space) i0_reciprocal	90240000.0000
Solution quality estimate total_estimate	0.7557
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.314
Kurtosis Kurtosis kurtosis	-0.969
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18190000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.481; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.503; Smooth: 0.875

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	L-PHENYLALANINE DEHYDROGENASE
Molecular weight formula_weight	36412.6 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	6119

SIDSALNWDGEMTVTRFDAMTGAHFVIRLDSTQLGPAAGGTRAAQYSNLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREASTTTATA

来源 Source

来源生物 organism	Rhodococcus sp.
NCBI Class编号 ncbi_taxonomy_id	1831
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	L-PHENYLALANINE DEHYDROGENASE
Molecular weight formula_weight	36442.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SIDSALNWDGEMTVTRFDSMTGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREASTTTATA

来源 Source

来源生物 organism	Rhodococcus sp.
NCBI Class编号 ncbi_taxonomy_id	1831
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	PHENYLALANINE
Molecular weight formula_weight	165.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	928

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1c1da1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1c1da2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d1c1db1
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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1c1db2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

CATH v4.4 (4 domains)

Domain ID domain_id	1c1dA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1c1dA02
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	1c1dB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	1c1dB02
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

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8. Citations (1)

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Unit-cell length a length_a	64.800 Å
Unit-cell length b length_b	110.600 Å
Unit-cell length c length_c	113.300 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1950
R_work r_work	0.1930
R_free r_free	0.2380

fit	/app/data/saxs_computation/c1/1c1d/1c1d.fit
pddf	/app/data/pr_computation/c1/1c1d/1c1d.pr.out
profile	/app/data/saxs_computation/c1/1c1d/1c1d.dat

L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE

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

L-PHENYLALANINE 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

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)