1xmi

Crystal structure of human F508A NBD1 domain with ATP

Method: X-RAY DIFFRACTION Dmax: 143.5 Å Quality: GOOD

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

Cystic fibrosis transmembrane conductance regulator

Homo sapiens

UniProt P13569

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 388–678 Chain B; UniProt 388–678 Chain C; UniProt 388–678 Chain D; UniProt 388–678 Chain E; UniProt 388–678 Fragment:nucleotide binding domain one Mutation:F508A MG MAGNESIUM ION × 5 ATP ADENOSINE-5'-TRIPHOSPHATE × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;277 K;PEG 400, glycerol, ethylene glycol, tris, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.25 Å R-free 0.265
2 Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 388–678 Chain B; UniProt 388–678 Chain C; UniProt 388–678 Chain D; UniProt 388–678 Chain E; UniProt 388–678 Fragment:nucleotide binding domain one Mutation:F508A MG MAGNESIUM ION × 10 ATP ADENOSINE-5'-TRIPHOSPHATE × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.5;277 K;PEG 400, glycerol, ethylene glycol, tris, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.25 Å R-free 0.265

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.

52 other PDB entries and 69 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CFTR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–291; UniProt 388–678 Author chain B; PDBConstruct 1–291; UniProt 388–678 Author chain C; PDBConstruct 1–291; UniProt 388–678 Author chain D; PDBConstruct 1–291; UniProt 388–678 Author chain E; PDBConstruct 1–291; UniProt 388–678

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 1xmi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1xmi
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1xmi
Deposition date deposition_date2004-10-02
Structure title titleCrystal structure of human F508A NBD1 domain with ATP
Keywords keywordsCFTR; NBD1 domain; F508A; cystic fibrosis; nucleotide-binding domain 1, MEMBRANE PROTEIN, HYDROLASE; MEMBRANE PROTEIN, HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.36
Radius of gyration Rg (electron density) rg_electron38.02
Forward intensity I(0) i0346725000.00
Molecular weight molecular_weight150210.0 kDa
Excluded volume excluded_volume187690 ų
Envelope volume envelope_volume256440 ų
Hydration-shell volume shell_volume56252 ų
Envelope diameter envelope_diameter148.1
Shell Rg shell_rg43.44
Envelope Rg envelope_rg38.42
Shape Rg shape_rg38.07
Total Rg total_rg38.18
Total atoms total_atoms10524
Residues n_residues1329
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 dmax143.5
Rg (real space) rg_real38.39
Rg uncertainty (real space) rg_real_error1.58
I(0) (real space) i0_real3.4670e+08
I(0) uncertainty (real space) i0_real_error6.6340e+06
Rg (reciprocal space) rg_reciprocal38.37
I(0) (reciprocal space) i0_reciprocal346700000.0000
Solution quality estimate total_estimate0.8427
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.5
Skewness Skewness skewness0.368
Kurtosis Kurtosis kurtosis-0.293
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56600000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.668; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1xmia1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like
Domain ID domain_idd1xmia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xmib1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like
Domain ID domain_idd1xmib2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xmic_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like
Domain ID domain_idd1xmid1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like
Domain ID domain_idd1xmid2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xmie_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.12 — ABC transporter ATPase domain-like

CATH v4.4 (5 domains)

Domain ID domain_id1xmiA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xmiB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xmiC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xmiD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xmiE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)