1d4o

CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 53.7 Å Quality: GOOD

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

NADP(H) TRANSHYDROGENASE

Bos taurus

UniProt P11024

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 903–1086 Fragment:NADP(H) BINDING DOMAIN NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.4;277 K;24% w/v MPEG 5000, 100mM sodium cacodylate and 200mM magnesium acetate., pH 7.4, VAPOR DIFFUSION, SITTING DROP Resolution 1.21 Å R-free 0.223

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name NNTM_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–184; UniProt 903–1086

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 1d4o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d4o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d4o
Deposition date deposition_date1999-10-04
Structure title titleCRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS RESOLUTION
Keywords keywordsNUCLEOTIDE-BINDING FOLD, PROTEIN-NADP(H) COMPLEX, INVERTED BINDING OF NADP(H), OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.40
Radius of gyration Rg (electron density) rg_electron15.00
Forward intensity I(0) i07639720.00
Molecular weight molecular_weight19838.0 kDa
Excluded volume excluded_volume24714 ų
Envelope volume envelope_volume27416 ų
Hydration-shell volume shell_volume15081 ų
Envelope diameter envelope_diameter54.8
Shell Rg shell_rg21.37
Envelope Rg envelope_rg15.36
Shape Rg shape_rg15.01
Total Rg total_rg16.09
Total atoms total_atoms1386
Residues n_residues177
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax53.7
Rg (real space) rg_real16.26
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real7.6400e+06
I(0) uncertainty (real space) i0_real_error8.9130e+04
Rg (reciprocal space) rg_reciprocal16.28
I(0) (reciprocal space) i0_reciprocal7640000.0000
Solution quality estimate total_estimate0.7870
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.0
Skewness Skewness skewness0.119
Kurtosis Kurtosis kurtosis-0.247
Angular range angular_range— – 0.4850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1833000.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.746; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d4oa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.4 — Transhydrogenase domain III (dIII)

CATH v4.4 (1 domains)

Domain ID domain_id1d4oA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain

8. Citations (1)

9. Files and Curves (10)