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1t6w

RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES

Method: SOLUTION NMR Dmax: 48.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

hypothetical protein XP_346638

Rattus norvegicus

UniProt P08921

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 23–121 Mutation：N15D, N17D CA CALCIUM ION × 1 SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Pressure 1 NMR sample composition：95% H2O, 5% D2O, protein 1 mM, KCl 130 mM, CaCl2 10 mM, PIPES 20 mM | 95% H2O/5% D2O Resolution not provided

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 1T6W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A64 ENGINEERING A MISFOLDED FORM OF RAT CD2 Deposited 1998-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–121（99 aa） Fragment：DOMAIN 1
Chain B 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；20% MPD, 200MM NACL, 0.1M NACO, PH 4.6
Resolution 2.00 Å R-free 0.273
1A6P ENGINEERING OF A MISFOLDED FORM OF CD2 Deposited 1998-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 26–121（96 aa） Fragment：DOMAIN 1
Chain B 26–121（96 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；20% PEG 4000, 5% GLYCEROL, 0.1M NACO, PH 4.6
Resolution 2.08 Å R-free 0.296
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 23–121（99 aa） Fragment：DOMAIN 1
Chain B 23–121（99 aa） Fragment：DOMAIN 1
Chain C 23–121（99 aa） Fragment：DOMAIN 1
Chain D 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5
Resolution 3.10 Å R-free 0.306
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–121（99 aa） Fragment：DOMAIN 1
Chain B 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5
Resolution 3.10 Å R-free 0.306
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 23–121（99 aa） Fragment：DOMAIN 1
Chain D 23–121（99 aa） Fragment：DOMAIN 1
Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5
Resolution 3.10 Å R-free 0.306
1CDC CD2, N-TERMINAL DOMAIN (1-99), TRUNCATED FORM Deposited 1995-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–121（99 aa）
Chain B 23–121（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1HNG CRYSTAL STRUCTURE AT 2.8 ANGSTROMS RESOLUTION OF A SOLUBLE FORM OF THE CELL ADHESION MOLECULE CD2 Deposited 1994-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 23–198（176 aa）
Chain B 23–198（176 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å

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

View Construct and Data Evidence
UniProt name CD2_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–99； UniProt 23–121

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 1t6w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t6w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t6w
Deposition date deposition_date2004-05-07
Structure title titleRATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES
Keywords keywordsCALCIUM-BINDING PROTEIN, CD2, DESIGN, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.69 Å
Radius of gyration Rg (electron density) rg_electron13.42 Å
Forward intensity I(0) i0700686000.00
Molecular weight molecular_weight223670.0 kDa
Excluded volume excluded_volume279820 ų
Envelope volume envelope_volume24672 ų
Hydration-shell volume shell_volume13689 ų
Envelope diameter envelope_diameter50.1 Å
Shell Rg shell_rg21.02 Å
Envelope Rg envelope_rg15.75 Å
Shape Rg shape_rg13.37 Å
Total Rg total_rg13.71 Å
Total atoms total_atoms31480
Residues n_residues1980
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 dmax48.0 Å
Rg (real space) rg_real13.67 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real7.0070e+08
I(0) uncertainty (real space) i0_real_error7.6780e+06
Rg (reciprocal space) rg_reciprocal13.67 Å
I(0) (reciprocal space) i0_reciprocal700700000.0000
Solution quality estimate total_estimate0.5922
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.4 Å
Skewness Skewness skewness0.302
Kurtosis Kurtosis kurtosis-0.190
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha320100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.648; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.982; Smooth: 0.000
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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id1t6wA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)