SAXSdb — 7m6u

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Carboxypeptidase G2 circular permuation pro-domain fusion

synthetic construct

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 89–415 Chain A； UniProt 25–88 Chain C； UniProt 89–415 Chain C； UniProt 25–88	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 89–415 Chain B； UniProt 25–88 Chain D； UniProt 89–415 Chain D； UniProt 25–88	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

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 7M6U	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 ligand/ion 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
6XJ5 Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design Deposited 2020-06-22	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 24–415（392 aa） Chain B 24–415（392 aa）	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
6XJ5 Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design Deposited 2020-06-22	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 C 24–415（392 aa） Chain D 24–415（392 aa）	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
6XJ5 Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design Deposited 2020-06-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 24–415（392 aa） Chain F 24–415（392 aa）	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
6XJ5 Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design Deposited 2020-06-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 24–415（392 aa） Chain H 24–415（392 aa）	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

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

View Construct and Data Evidence

UniProt name	CBPG_PSES6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–350； UniProt 89–415 Author chain A； PDBConstruct 355–418； UniProt 25–88 Author chain B； PDBConstruct 24–350； UniProt 89–415 Author chain B； PDBConstruct 355–418； UniProt 25–88 Author chain C； PDBConstruct 24–350； UniProt 89–415 Author chain C； PDBConstruct 355–418； UniProt 25–88 Author chain D； PDBConstruct 24–350； UniProt 89–415 Author chain D； PDBConstruct 355–418； UniProt 25–88

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7m6u
Deposition date deposition_date	2021-03-26
Structure title title	Crystal structure of a circular permutation and computationally designed pro-enzyme of carboxypeptidase G2
Keywords keywords	pro-enzyme, enzyme design, directed enzyme-prodrug therapy, methotrexate, circular permutation, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	42.33 Å
Radius of gyration Rg (electron density) rg_electron	42.31 Å
Forward intensity I(0) i0	394687000.00
Molecular weight molecular_weight	156630.0 kDa
Excluded volume excluded_volume	193730 Å³
Envelope volume envelope_volume	281000 Å³
Hydration-shell volume shell_volume	58020 Å³
Envelope diameter envelope_diameter	173.5 Å
Shell Rg shell_rg	45.13 Å
Envelope Rg envelope_rg	41.78 Å
Shape Rg shape_rg	42.25 Å
Total Rg total_rg	42.65 Å
Total atoms total_atoms	10973
Residues n_residues	1528
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	168.3 Å
Rg (real space) rg_real	42.48 Å
Rg uncertainty (real space) rg_real_error	2.29 Å
I(0) (real space) i0_real	3.9470e+08
I(0) uncertainty (real space) i0_real_error	8.6690e+06
Rg (reciprocal space) rg_reciprocal	42.34 Å
I(0) (reciprocal space) i0_reciprocal	394600000.0000
Solution quality estimate total_estimate	0.7815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.6 Å
Skewness Skewness skewness	0.542
Kurtosis Kurtosis kurtosis	0.412
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24820000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.407; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Carboxypeptidase G2 circular permuation pro-domain fusion
Molecular weight formula_weight	47217.3 kDa
EC 编号 ec_number	3.4.17.11
Mutation mutation	K177A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11105

MGSSHHHHHHSSGLVPRGSHMGSLVVGDNIVGKIKGRGGKNLLLMSHMDTVYLKGILAKAPFRVEGDKAYGPGIADDKGGNAVILHTLKLLKEYGVRDYGTITVLFNTDEEAGSFGSRDLIQEEAKLADYVLSFEPTSAGDEKLSLGTSGIAYVQVNITGKASHAGAAPELGVNALVEASDLVLRTMNIDDKAKNLRFNWTIAKAGNVSNIIPASATLNADVRYARNEDFDAAMKTLEERAQQKKLPEADVKVIVTRGRPAFNAGEGGKKLVDKAVAYYKEAGGTLGVEERTGGGTDAAYAALSGKPVIESLGLPGFGYHSDKAEYVDISAIPRRLYMAARLIMDLGAGKGTASAQKRDNVLFQAATDEQPAVIKTLEKLVNIETGTGDAEGIAAAGNFLEAELKNLGFTVTRSKSAGGSPLGMWSRGSAEAAWKEAEAKDWAAKA

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	132

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8. Citations (2)

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Unit-cell length a length_a	78.540 Å
Unit-cell length b length_b	106.360 Å
Unit-cell length c length_c	121.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	39.270 Å
R factor r_factor	0.2245
R_work r_work	0.2217
R_free r_free	0.2792

fit	/app/data/saxs_computation/m6/7m6u/7m6u.fit
pddf	/app/data/pr_computation/m6/7m6u/7m6u.pr.out
profile	/app/data/saxs_computation/m6/7m6u/7m6u.dat

Crystal structure of a circular permutation and computationally designed pro-enzyme of carboxypeptidase G2

1. Protein Identity and Related Structures Protein Identity & Related Structures

Carboxypeptidase G2 circular permuation pro-domain fusion

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction