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6xj5

Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design

Method: X-RAY DIFFRACTION Dmax: 170.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Carboxypeptidase G2

Pseudomonas sp. (strain RS-16)

UniProt P06621

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 24–415 Chain B； UniProt 24–415 Mutation：S203C Mutation：S203C Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 12 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Reservoir consisted of 750 uL of 0.2 M Tris pH 7.5, 10% PEG 3350, and 5% glycerol. 2 uL of reservoir solution was mixed with 2 uL of protein solution, consisting of 4.7 mg/mL CPG2 in 50 mM Tris 100 mM NaCl pH 7.4 supplemented with 0.1 M ZnSO4 Resolution 3.11 Å R-free 0.309
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 24–415 Chain D； UniProt 24–415 Mutation：S203C Mutation：S203C Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 14 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Reservoir consisted of 750 uL of 0.2 M Tris pH 7.5, 10% PEG 3350, and 5% glycerol. 2 uL of reservoir solution was mixed with 2 uL of protein solution, consisting of 4.7 mg/mL CPG2 in 50 mM Tris 100 mM NaCl pH 7.4 supplemented with 0.1 M ZnSO4 Resolution 3.11 Å R-free 0.309
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 24–415 Chain F； UniProt 24–415 Mutation：S203C Mutation：S203C Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 17 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Reservoir consisted of 750 uL of 0.2 M Tris pH 7.5, 10% PEG 3350, and 5% glycerol. 2 uL of reservoir solution was mixed with 2 uL of protein solution, consisting of 4.7 mg/mL CPG2 in 50 mM Tris 100 mM NaCl pH 7.4 supplemented with 0.1 M ZnSO4 Resolution 3.11 Å R-free 0.309
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 24–415 Chain H； UniProt 24–415 Mutation：S203C Mutation：S203C Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 13 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Reservoir consisted of 750 uL of 0.2 M Tris pH 7.5, 10% PEG 3350, and 5% glycerol. 2 uL of reservoir solution was mixed with 2 uL of protein solution, consisting of 4.7 mg/mL CPG2 in 50 mM Tris 100 mM NaCl pH 7.4 supplemented with 0.1 M ZnSO4 Resolution 3.11 Å R-free 0.309

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 6XJ5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CG2 CARBOXYPEPTIDASE G2 Deposited 1996-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 23–415（393 aa）
Chain B 23–415（393 aa）
Chain C 23–415（393 aa）
Chain D 23–415（393 aa）
Not recorded ZN ZINC ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；HANGING DROPS WERE FORMED BY MIXING 4 MICROLITERS OF PROTEIN SOLUTION AT 16-20 MG/ML WITH 4 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 10-12% PEG 4000, 0.2M TRIS (PH 7.2), 0.2M ZINC ACETATE 10% GLYCEROL. CRYSTALS GREW AT 18-20 DEGREES WITHIN A FEW DAYS., vapor diffusion - hanging drop, temperature 291K
Resolution 2.50 Å R-free 0.224
7M6U Crystal structure of a circular permutation and computationally designed pro-enzyme of carboxypeptidase G2 Deposited 2021-03-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 89–415（327 aa）
Chain A 25–88（64 aa）
Chain C 89–415（327 aa）
Chain C 25–88（64 aa）
Mutation：K177A Mutation：K177A Mutation：K177A Mutation：K177A ZN ZINC ION × 11 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Protein was prepared to a concentration of 19 mg/mL in 50 mM Tris 100 mM NaCl pH 7.4 0.2 mM ZnSO4. Reservoirs containing 750 uL of 20 mM Tris pH 8.0, 10% glycerol, and 10% PEG 3350 were prepared in 24 well hanging drop vapor diffusion plates. Equal volumes of protein solution and reservoir solution were mixed on a cover slip and suspended over the reservoir
Resolution 2.59 Å R-free 0.279
7M6U Crystal structure of a circular permutation and computationally designed pro-enzyme of carboxypeptidase G2 Deposited 2021-03-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 89–415（327 aa）
Chain B 25–88（64 aa）
Chain D 89–415（327 aa）
Chain D 25–88（64 aa）
Mutation：K177A Mutation：K177A Mutation：K177A Mutation：K177A ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Protein was prepared to a concentration of 19 mg/mL in 50 mM Tris 100 mM NaCl pH 7.4 0.2 mM ZnSO4. Reservoirs containing 750 uL of 20 mM Tris pH 8.0, 10% glycerol, and 10% PEG 3350 were prepared in 24 well hanging drop vapor diffusion plates. Equal volumes of protein solution and reservoir solution were mixed on a cover slip and suspended over the reservoir
Resolution 2.59 Å R-free 0.279

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CBPG_PSES6
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 20–411； UniProt 24–415 Author chain C； PDBConstruct 20–411； UniProt 24–415 Author chain E； PDBConstruct 20–411； UniProt 24–415 Author chain G； PDBConstruct 20–411； UniProt 24–415 Author chain B； PDBConstruct 20–411； UniProt 24–415 Author chain D； PDBConstruct 20–411； UniProt 24–415 Author chain F； PDBConstruct 20–411； UniProt 24–415 Author chain H； PDBConstruct 20–411； UniProt 24–415

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 6xj5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xj5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xj5
Deposition date deposition_date2020-06-22
Structure title titleCarboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design
Keywords keywordsmetalloprotein design, bivalent metal ion co-ordination, bis-imidazoles, bioconjugation, 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_guinier51.74 Å
Radius of gyration Rg (electron density) rg_electron51.66 Å
Forward intensity I(0) i01442470000.00
Molecular weight molecular_weight306240.0 kDa
Excluded volume excluded_volume378150 ų
Envelope volume envelope_volume577770 ų
Hydration-shell volume shell_volume93797 ų
Envelope diameter envelope_diameter174.7 Å
Shell Rg shell_rg55.95 Å
Envelope Rg envelope_rg49.27 Å
Shape Rg shape_rg51.66 Å
Total Rg total_rg51.80 Å
Total atoms total_atoms21421
Residues n_residues3103
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 dmax170.9 Å
Rg (real space) rg_real51.60 Å
Rg uncertainty (real space) rg_real_error1.62 Å
I(0) (real space) i0_real1.4420e+09
I(0) uncertainty (real space) i0_real_error2.7670e+07
Rg (reciprocal space) rg_reciprocal51.83 Å
I(0) (reciprocal space) i0_reciprocal1443000000.0000
Solution quality estimate total_estimate0.8880
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary62.7 Å
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha84910000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.880
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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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8. Citations (1)

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9. Files and Curves (10)