3cev

ARGINASE FROM BACILLUS CALDEVELOX, COMPLEXED WITH L-ARGININE

Method: X-RAY DIFFRACTION Dmax: 164.2 Å Quality: GOOD

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

PROTEIN (ARGINASE)

Bacillus caldovelox

UniProt P53608

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–299 Chain B; UniProt 2–299 Chain C; UniProt 2–299 Not recorded MN MANGANESE (II) ION × 6 ARG ARGININE × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5 RESERVOIR SOLUTION 28% MONOMETHYLPEG 2000, 10 MM EDTA, 10 MM GUANIDINE HYDROCHLORIDE, IN 0.05 M BISTRISPROPANE/HCL, PH 8. THE CRYSTALS WERE THEN SOAKED IN 42.5% MMPEG 2000, 10 MM GUANIDINE HYDROCHLORIDE, 10 MM L-ARGININE, 10 MM EDTA, 0.05M BISTRISPROPANE/HCL, PH 8.5 FOR 8 HOURS, VAPOR DIFFUSION, HANGING DROP Resolution 2.40 Å R-free 0.243
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 2–299 Chain E; UniProt 2–299 Chain F; UniProt 2–299 Not recorded MN MANGANESE (II) ION × 3 ARG ARGININE × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5 RESERVOIR SOLUTION 28% MONOMETHYLPEG 2000, 10 MM EDTA, 10 MM GUANIDINE HYDROCHLORIDE, IN 0.05 M BISTRISPROPANE/HCL, PH 8. THE CRYSTALS WERE THEN SOAKED IN 42.5% MMPEG 2000, 10 MM GUANIDINE HYDROCHLORIDE, 10 MM L-ARGININE, 10 MM EDTA, 0.05M BISTRISPROPANE/HCL, PH 8.5 FOR 8 HOURS, VAPOR DIFFUSION, HANGING DROP Resolution 2.40 Å R-free 0.243
3 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 2–299 Chain E; UniProt 2–299 Chain F; UniProt 2–299 Not recorded MN MANGANESE (II) ION × 6 ARG ARGININE × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5 RESERVOIR SOLUTION 28% MONOMETHYLPEG 2000, 10 MM EDTA, 10 MM GUANIDINE HYDROCHLORIDE, IN 0.05 M BISTRISPROPANE/HCL, PH 8. THE CRYSTALS WERE THEN SOAKED IN 42.5% MMPEG 2000, 10 MM GUANIDINE HYDROCHLORIDE, 10 MM L-ARGININE, 10 MM EDTA, 0.05M BISTRISPROPANE/HCL, PH 8.5 FOR 8 HOURS, VAPOR DIFFUSION, HANGING DROP Resolution 2.40 Å R-free 0.243

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.

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

View Construct and Data Evidence
UniProt name ARGI_BACCD
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–299; UniProt 2–299 Author chain B; PDBConstruct 2–299; UniProt 2–299 Author chain C; PDBConstruct 2–299; UniProt 2–299 Author chain D; PDBConstruct 2–299; UniProt 2–299 Author chain E; PDBConstruct 2–299; UniProt 2–299 Author chain F; PDBConstruct 2–299; UniProt 2–299

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 3cev

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3cev
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cev
Deposition date deposition_date1999-03-15
Structure title titleARGINASE FROM BACILLUS CALDEVELOX, COMPLEXED WITH L-ARGININE
Keywords keywordsENZYME, HYDROLASE, ARGININE HYDROLYSIS, NITROGEN METABOLISM, MANGANESE METALLOENZYME; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier53.01
Radius of gyration Rg (electron density) rg_electron53.40
Forward intensity I(0) i0565005000.00
Molecular weight molecular_weight196180.0 kDa
Excluded volume excluded_volume245160 ų
Envelope volume envelope_volume329910 ų
Hydration-shell volume shell_volume53455 ų
Envelope diameter envelope_diameter173.6
Shell Rg shell_rg52.13
Envelope Rg envelope_rg52.28
Shape Rg shape_rg53.42
Total Rg total_rg53.28
Total atoms total_atoms13758
Residues n_residues1788
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax164.2
Rg (real space) rg_real53.40
Rg uncertainty (real space) rg_real_error1.63
I(0) (real space) i0_real5.6500e+08
I(0) uncertainty (real space) i0_real_error1.0520e+07
Rg (reciprocal space) rg_reciprocal52.66
I(0) (reciprocal space) i0_reciprocal564400000.0000
Solution quality estimate total_estimate0.7780
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.3
Skewness Skewness skewness0.382
Kurtosis Kurtosis kurtosis-0.827
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16680000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.734; Smooth: 0.001

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3ceva_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd3cevb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd3cevc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd3cevd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd3ceve_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd3cevf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases

CATH v4.4 (6 domains)

Domain ID domain_id3cevA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id3cevB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id3cevC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id3cevD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id3cevE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id3cevF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain

8. Citations (1)

9. Files and Curves (10)