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1gkm

HISTIDINE AMMONIA-LYASE (HAL) FROM PSEUDOMONAS PUTIDA INHIBITED WITH L-CYSTEINE

Method: X-RAY DIFFRACTION Dmax: 74.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histidine ammonia-lyase

Pseudomonas putida

UniProt P21310

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 B； UniProt 2–510 Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) CYS CYSTEINE × 4 SO4 SULFATE ION × 4 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.1；CRYSTALLIZED FROM 2.0 M (NH4) 2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 25 % (V/V) GLYCEROL WERE USED AS CRYOPROTECTANT Resolution 1.00 Å R-free 0.135

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 1GKM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B8F Histidine ammonia-lyase (HAL) from Pseudomonas putida Deposited 1999-01-31 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 2–510（509 aa）
Mutation：C273A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.1；CRYSTALLIZED FROM 2.0 M (NH4)2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT pH 8.1. 20 % (V/V) GLYCEROL WERE USED AS CRYOPROTECTANT
Resolution 2.10 Å R-free 0.263
1EB4 Histidine Ammonia-Lyase (HAL) Mutant F329A from Pseudomonas putida Deposited 2001-07-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–510（509 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.1；2.0 M (NH4)2 SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 20 % (V/V) GLYCEROL USED AS CRYOPROTECTANT
Resolution 2.00 Å R-free 0.232
1GK2 Histidine Ammonia-Lyase (HAL) Mutant F329G from Pseudomonas putida Deposited 2001-08-07 Different construct 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 2–510（509 aa）
Chain B 2–510（509 aa）
Chain C 2–510（509 aa）
Chain D 2–510（509 aa）
Mutation：YES Mutation：YES Mutation：YES Mutation：YES GOL GLYCEROL × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.1；CRYSTALLIZED FROM 2.0 M (NH4)2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 20 % (V/V) GLYCEROL WERE USED AS CRYOPROTECTANT
Resolution 1.90 Å R-free 0.226
1GK3 Histidine Ammonia-Lyase (HAL) Mutant D145A from Pseudomonas putida Deposited 2001-08-07 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 2–510（509 aa）
Mutation：YES SO4 SULFATE ION × 4 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.1；CRYSTALLIZED FROM 2.0 M (NH4)2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 20 % (V/V) GLYCEROL WERE USED AS CRYOPROTECTANT
Resolution 2.25 Å R-free 0.280
1GKJ Histidine Ammonia-Lyase (HAL) Mutant Y280F from Pseudomonas putida Deposited 2001-08-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–510（509 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.1；CRYSTALLIZED FROM 2.0 M (NH4)2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 20 % (V/V) GLYCEROL WERE USED AS CRYOPROTECTANT
Resolution 1.70 Å R-free 0.236

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

View Construct and Data Evidence
UniProt name HUTH_PSEPU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–507； UniProt 2–510

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 1gkm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1gkm
Deposition date deposition_date2001-08-16
Structure title titleHISTIDINE AMMONIA-LYASE (HAL) FROM PSEUDOMONAS PUTIDA INHIBITED WITH L-CYSTEINE
Keywords keywordsLYASE, HISTIDINE DEGRADATION; 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_guinier27.23 Å
Radius of gyration Rg (electron density) rg_electron26.58 Å
Forward intensity I(0) i048681600.00
Molecular weight molecular_weight53878.0 kDa
Excluded volume excluded_volume67382 ų
Envelope volume envelope_volume79632 ų
Hydration-shell volume shell_volume26097 ų
Envelope diameter envelope_diameter96.9 Å
Shell Rg shell_rg32.53 Å
Envelope Rg envelope_rg26.90 Å
Shape Rg shape_rg26.58 Å
Total Rg total_rg27.21 Å
Total atoms total_atoms3781
Residues n_residues506
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 dmax74.2 Å
Rg (real space) rg_real26.04 Å
Rg uncertainty (real space) rg_real_error0.16 Å
I(0) (real space) i0_real4.6720e+07
I(0) uncertainty (real space) i0_real_error5.0720e+05
Rg (reciprocal space) rg_reciprocal27.37 Å
I(0) (reciprocal space) i0_reciprocal48680000.0000
Solution quality estimate total_estimate0.6800
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.9 Å
Skewness Skewness skewness0.398
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha1.9550
Highest regularization parameter α highest_alpha9357000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.968; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000
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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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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1gkma_
Class classa — All alpha proteins
Fold Fold folda.127 — L-aspartase-like
Superfamily Superfamily superfamilya.127.1 — L-aspartase-like
Family Family familya.127.1.2 — HAL/PAL-like
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8. Citations (3)

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9. Files and Curves (10)