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4itx

P113S mutant of E. coli Cystathionine beta-lyase MetC inhibited by reaction with L-Ala-P

Method: X-RAY DIFFRACTION Dmax: 105.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cystathionine beta-lyase MetC

Escherichia coli

UniProt P06721

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–395 Chain B； UniProt 1–395 Mutation：P113S IN5 {1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.61 Å R-free 0.195

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 4ITX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CL1 CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI Deposited 1997-09-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa）
Chain B 1–395（395 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) BCT BICARBONATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.2；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2)
Resolution 1.83 Å R-free 0.221
1CL2 CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINE Deposited 1997-09-04 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa）
Chain B 1–395（395 aa）
Not recorded PPG (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.2；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2)
Resolution 2.20 Å
2FQ6 Cystathionine beta-lyase (cbl) from escherichia coli in complex with n-hydrazinocarbonylmethyl-2-trifluoromethyl-benzamide Deposited 2006-01-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa）
Chain B 1–395（395 aa）
Not recorded P3F PHOSPHORIC ACID MONO-(5-HYDROXY-6-METHYL-4-{[2-(2-TRIFLUOROMETHYL-BENZOYLAMINO)-ACETYL]-HYDRAZONOMETHYL}-PYRIDIN-3-YLMETHYL)ESTER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.1M Hepes, 0.15M calcium chloride, 26% PEG 400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.78 Å R-free 0.225
2GQN Cystathionine Beta-Lyase (CBL) from Escherichia Coli in complex with N-Hydrazinocarbonylmethyl-2-Nitro-Benzamide Deposited 2006-04-21 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa）
Chain B 1–395（395 aa）
Not recorded BLP (5-HYDROXY-6-METHYL-4-((2-(2-(2-NITROBENZAMIDO)ACETYL)HYDRAZINYL)METHYL)PYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.1M Hepes, 0.15M calcium chloride, and 26% PEG400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.227
4ITG P113S mutant of E. coli Cystathionine beta-lyase MetC Deposited 2013-01-18 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa）
Chain B 1–395（395 aa）
Mutation：P113S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：P113S Non-standard monomer：Yes (specific site not provided by mmCIF) EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.74 Å R-free 0.198

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

View Construct and Data Evidence
UniProt name METC_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 1–395； UniProt 1–395

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 4itx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4itx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4itx
Deposition date deposition_date2013-01-19
Structure title titleP113S mutant of E. coli Cystathionine beta-lyase MetC inhibited by reaction with L-Ala-P
Keywords keywordsCystathionine beta-lyase, LYASE; LYASE
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_guinier33.70 Å
Radius of gyration Rg (electron density) rg_electron33.35 Å
Forward intensity I(0) i0114896000.00
Molecular weight molecular_weight85903.0 kDa
Excluded volume excluded_volume107350 ų
Envelope volume envelope_volume135920 ų
Hydration-shell volume shell_volume33511 ų
Envelope diameter envelope_diameter105.7 Å
Shell Rg shell_rg41.09 Å
Envelope Rg envelope_rg32.64 Å
Shape Rg shape_rg33.39 Å
Total Rg total_rg33.78 Å
Total atoms total_atoms6042
Residues n_residues783
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 dmax105.3 Å
Rg (real space) rg_real33.73 Å
Rg uncertainty (real space) rg_real_error0.98 Å
I(0) (real space) i0_real1.1490e+08
I(0) uncertainty (real space) i0_real_error1.9630e+06
Rg (reciprocal space) rg_reciprocal33.71 Å
I(0) (reciprocal space) i0_reciprocal114900000.0000
Solution quality estimate total_estimate0.8803
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.9 Å
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.827
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha36100000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.879; Smooth: 0.854
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4itxa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.3 — Cystathionine synthase-like
Domain ID domain_idd4itxb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.3 — Cystathionine synthase-like

CATH v4.4 (4 domains)

Domain ID domain_id4itxA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
Domain ID domain_id4itxA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id4itxB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
Domain ID domain_id4itxB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
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8. Citations (1)

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9. Files and Curves (10)