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1tf9

Streptomyces griseus aminopeptidase complexed with P-Iodo-L-Phenylalanine

Method: X-RAY DIFFRACTION Dmax: 55.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Aminopeptidase

OrganismNot specified

UniProt P80561

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 1–284 Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 PHI IODO-PHENYLALANINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.30 Å R-free 0.172

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 1TF9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CP7 AMINOPEPTIDASE FROM STREPTOMYCES GRISEUS Deposited 1999-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；16% PEG 4K, 0.1 M SODIUM ACETATE PH 5.5
Resolution 1.58 Å R-free 0.171
1F2O CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE Deposited 2000-05-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 LEU LEUCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG4000, Ammunium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.175
1F2P CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-PHENYLALANINE Deposited 2000-05-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 PHE PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG4000, Sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.225
1QQ9 STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH METHIONINE Deposited 1999-06-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 MET METHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 4000, AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.53 Å R-free 0.173
1TF8 Streptomyces griseus aminopeptidase complexed with L-tryptophan Deposited 2004-05-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 TRP TRYPTOPHAN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.30 Å R-free 0.174
1TKF Streptomyces griseus aminopeptidase complexed with D-tryptophan Deposited 2004-06-08 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 DTR D-TRYPTOPHAN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.20 Å R-free 0.168
1TKH Streptomyces griseus aminopeptidase complexed with D-Phenylalanine Deposited 2004-06-08 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 DPN D-PHENYLALANINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.156
1TKJ Streptomyces griseus aminopeptidase complexed with D-Methionine Deposited 2004-06-08 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 MED D-METHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.15 Å R-free 0.151
1XBU Streptomyces griseus aminopeptidase complexed with p-iodo-D-phenylalanine Deposited 2004-08-31 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–277（277 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 IOY P-IODO-D-PHENYLALANINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.20 Å R-free 0.167
1XJO STRUCTURE OF AMINOPEPTIDASE Deposited 1996-10-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–284（284 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 PO4 PHOSPHATE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；16% PEG 4K, 0.1 M SODIUM ACETATE, pH 5.5
Resolution 1.75 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APX_STRGR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–284； UniProt 1–284

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 1tf9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1tf9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1tf9
Deposition date deposition_date2004-05-27
Structure title titleStreptomyces griseus aminopeptidase complexed with P-Iodo-L-Phenylalanine
Keywords keywordsDOUBLE-ZINC METALLOPROTEINASE, CALCIUM ACTIVATION, PROTEIN-INHIBITOR COMPLEX, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.01 Å
Radius of gyration Rg (electron density) rg_electron16.91 Å
Forward intensity I(0) i016203500.00
Molecular weight molecular_weight29352.0 kDa
Excluded volume excluded_volume36108 ų
Envelope volume envelope_volume38692 ų
Hydration-shell volume shell_volume18633 ų
Envelope diameter envelope_diameter55.4 Å
Shell Rg shell_rg23.64 Å
Envelope Rg envelope_rg17.23 Å
Shape Rg shape_rg16.90 Å
Total Rg total_rg17.84 Å
Total atoms total_atoms2059
Residues n_residues275
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 dmax55.3 Å
Rg (real space) rg_real17.87 Å
Rg uncertainty (real space) rg_real_error0.24 Å
I(0) (real space) i0_real1.6200e+07
I(0) uncertainty (real space) i0_real_error1.8430e+05
Rg (reciprocal space) rg_reciprocal17.89 Å
I(0) (reciprocal space) i0_reciprocal16200000.0000
Solution quality estimate total_estimate0.9011
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.8 Å
Skewness Skewness skewness0.127
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4328000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1tf9a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
Family Family familyc.56.5.4 — Bacterial dinuclear zinc exopeptidases

CATH v4.4 (1 domains)

Domain ID domain_id1tf9A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
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8. Citations (1)

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9. Files and Curves (10)