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1z12

Crystal Structure of Bovine Low Molecular Weight PTPase Complexed with Vanadate

Method: X-RAY DIFFRACTION Dmax: 51.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Low molecular weight phosphotyrosine protein phosphatase

Bos taurus

UniProt P11064

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 1–157 Not recorded VO4 VANADATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG 4000, HEPES, Isopropanol, Na2VO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.20 Å

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 1Z12 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BVH SOLUTION STRUCTURE OF A LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE Deposited 1994-05-03 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–157（157 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1C0E Active Site S19A Mutant of Bovine Heart Phosphotyrosyl Phosphatase Deposited 1999-07-15 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 1–157（157 aa）
Mutation：S19A PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 4000, TRIS BUFFER, pH 7.00
Resolution 2.20 Å R-free 0.244
1C0E Active Site S19A Mutant of Bovine Heart Phosphotyrosyl Phosphatase Deposited 1999-07-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–157（157 aa）
Mutation：S19A PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 4000, TRIS BUFFER, pH 7.00
Resolution 2.20 Å R-free 0.244
1DG9 CRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT PTPASE COMPLEXED WITH HEPES Deposited 1999-11-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–157（157 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；20% PEG4k, 10% 2-propanol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION
Resolution 1.90 Å
1PHR THE CRYSTAL STRUCTURE OF A LOW MOLECULAR PHOSPHOTYROSINE PROTEIN PHOSPHATASE Deposited 1994-07-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–157（157 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.232
1PNT CRYSTAL STRUCTURE OF BOVINE HEART PHOSPHOTYROSYL PHOSPHATASE AT 2.2 ANGSTROMS RESOLUTION Deposited 1994-08-05 Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–157（157 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1Z13 Crystal Structure of Bovine Low Molecular Weight PTPase Complexed with Molybdate Deposited 2005-03-03 Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–157（157 aa）
Not recorded MOO MOLYBDATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG 4000, HEPES, Isopropanol, Na2MoO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.20 Å
5JNV Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with HEPES Deposited 2016-04-30 Different construct 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 2–158（157 aa）
Mutation：W49Y N50E EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 DMS DIMETHYL SULFOXIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；20% PEG 3350, 0.2 M NaCl, Bis Tris, HEPES
Resolution 1.60 Å R-free 0.200
5JNW Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with vanadate and uncompetitive inhibitor Deposited 2016-04-30 Different construct 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 2–158（157 aa）
Mutation：W49Y N50E VO4 VANADATE ION × 1 6LJ 2-(4-{[3-(piperidin-1-yl)propyl]amino}quinolin-2-yl)benzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；20% PEG 3350, 0.2 M NaCl, Bis Tris
Resolution 1.86 Å R-free 0.209

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PPAC_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–157； UniProt 1–157

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 1z12

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1z12
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1z12
Deposition date deposition_date2005-03-03
Structure title titleCrystal Structure of Bovine Low Molecular Weight PTPase Complexed with Vanadate
Keywords keywordsPTPase, Vanadate 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_guinier16.12 Å
Radius of gyration Rg (electron density) rg_electron14.92 Å
Forward intensity I(0) i06740160.00
Molecular weight molecular_weight18021.0 kDa
Excluded volume excluded_volume22204 ų
Envelope volume envelope_volume24884 ų
Hydration-shell volume shell_volume13980 ų
Envelope diameter envelope_diameter52.2 Å
Shell Rg shell_rg20.94 Å
Envelope Rg envelope_rg15.36 Å
Shape Rg shape_rg14.93 Å
Total Rg total_rg15.95 Å
Total atoms total_atoms1260
Residues n_residues157
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 dmax51.9 Å
Rg (real space) rg_real16.01 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real6.7400e+06
I(0) uncertainty (real space) i0_real_error7.0890e+04
Rg (reciprocal space) rg_reciprocal16.02 Å
I(0) (reciprocal space) i0_reciprocal6740000.0000
Solution quality estimate total_estimate0.8103
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.0 Å
Skewness Skewness skewness0.152
Kurtosis Kurtosis kurtosis-0.372
Angular range angular_range— – 0.4950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1305000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1z12a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.44 — Phosphotyrosine protein phosphatases I-like
Superfamily Superfamily superfamilyc.44.1 — Phosphotyrosine protein phosphatases I
Family Family familyc.44.1.1 — Low-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (1 domains)

Domain ID domain_id1z12A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (1)

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9. Files and Curves (10)