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1oib

PHOSPHATE-BINDING PROTEIN MUTANT T141D

Method: X-RAY DIFFRACTION Dmax: 122.1 Å Quality: SUSPICIOUS
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHATE-BINDING PROTEIN

Escherichia coli

UniProt P06128

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 26–346 Mutation：T141D No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 26–346 Mutation：T141D No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.40 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 1OIB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A40 PHOSPHATE-BINDING PROTEIN WITH ALA 197 REPLACED WITH TRP Deposited 1998-02-10 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 26–346（321 aa）
Mutation：A197W PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 1.70 Å R-free 0.269
1A55 PHOSPHATE-BINDING PROTEIN MUTANT A197C Deposited 1998-02-19 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 26–346（321 aa）
Mutation：A197C 2HP DIHYDROGENPHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.40 Å R-free 0.227
1IXG PHOSPHATE-BINDING PROTEIN MUTANT WITH THR 141 REPLACED BY ASP (T141D), COMPLEXED WITH PHOSPATE Deposited 1996-08-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–346（321 aa）
Mutation：T141D PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 1.05 Å R-free 0.139
1IXH PHOSPHATE-BINDING PROTEIN (PBP) COMPLEXED WITH PHOSPHATE Deposited 1996-08-01 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 26–346（321 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 0.98 Å R-free 0.141
1IXI PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 56 REPLACED BY ASN COMPLEX WITH MONOBASIC PHOSPHATE ION Deposited 1996-10-17 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 26–346（321 aa）
Mutation：D56N 2HP DIHYDROGENPHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 1.89 Å R-free 0.294
1PBP FINE TUNING OF THE SPECIFICITY OF THE PERIPLASMIC PHOSPHATE TRANSPORT RECEPTOR: SITE-DIRECTED MUTAGENESIS, LIGAND BINDING, AND CRYSTALLOGRAPHIC STUDIES Deposited 1994-07-20 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–346（321 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1QUI PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY GLY COMPLEX WITH BROMINE AND PHOSPHATE Deposited 1995-11-11 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–346（321 aa）
Mutation：D137G BR BROMIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.218
1QUJ PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY GLY COMPLEX WITH CHLORINE AND PHOSPHATE Deposited 1995-11-11 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–346（321 aa）
Mutation：D137G CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.209
1QUK PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY ASN COMPLEX WITH PHOSPHATE Deposited 1995-11-11 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–346（321 aa）
Mutation：D137N PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.189
1QUL PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 137 REPLACED BY THR COMPLEX WITH CHLORINE AND PHOSPHATE Deposited 1995-11-11 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–346（321 aa）
Mutation：D137T PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.205
2ABH PHOSPHATE-BINDING PROTEIN (RE-REFINED) Deposited 1995-11-28 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–346（321 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PSTS_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–321； UniProt 26–346 Author chain B； PDBConstruct 1–321； UniProt 26–346

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 1oib

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1oib
Deposition date deposition_date1995-11-25
Structure title titlePHOSPHATE-BINDING PROTEIN MUTANT T141D
Keywords keywordsPHOSPHATE TRANSPORT; PHOSPHATE TRANSPORT
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_guinier37.62 Å
Radius of gyration Rg (electron density) rg_electron38.19 Å
Forward intensity I(0) i069104400.00
Molecular weight molecular_weight68870.0 kDa
Excluded volume excluded_volume86864 ų
Envelope volume envelope_volume114360 ų
Hydration-shell volume shell_volume26233 ų
Envelope diameter envelope_diameter130.4 Å
Shell Rg shell_rg41.56 Å
Envelope Rg envelope_rg37.45 Å
Shape Rg shape_rg38.13 Å
Total Rg total_rg38.62 Å
Total atoms total_atoms4878
Residues n_residues642
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 dmax122.1 Å
Rg (real space) rg_real38.15 Å
Rg uncertainty (real space) rg_real_error1.37 Å
I(0) (real space) i0_real6.9100e+07
I(0) uncertainty (real space) i0_real_error1.1520e+06
Rg (reciprocal space) rg_reciprocal37.83 Å
I(0) (reciprocal space) i0_reciprocal69080000.0000
Solution quality estimate total_estimate0.4948
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.2 Å
Skewness Skewness skewness0.455
Kurtosis Kurtosis kurtosis-0.684
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11700000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.596; Stabil: 1.000; Sysdev: 0.020; Positv: 1.000; Valcen: 0.474; Smooth: 0.109
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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) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1oiba_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like
Domain ID domain_idd1oibb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id1oibA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1oibA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1oibB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1oibB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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8. Citations (3)

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9. Files and Curves (10)