SAXSdb — 1gk2

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

HISTIDINE AMMONIA-LYASE

PSEUDOMONAS PUTIDA

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 2–510 Chain B； UniProt 2–510 Chain C； UniProt 2–510 Chain D； UniProt 2–510	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

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 1GK2	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 construct Different mutation/modification 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 construct Different mutation/modification 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
1GK3 Histidine Ammonia-Lyase (HAL) Mutant D145A from Pseudomonas putida Deposited 2001-08-07	Different construct Different mutation/modification 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 construct Different mutation/modification 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
1GKM HISTIDINE AMMONIA-LYASE (HAL) FROM PSEUDOMONAS PUTIDA INHIBITED WITH L-CYSTEINE Deposited 2001-08-16	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 B 2–510（509 aa）	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

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 A； PDBConstruct 1–509； UniProt 2–510 Author chain B； PDBConstruct 1–509； UniProt 2–510 Author chain C； PDBConstruct 1–509； UniProt 2–510 Author chain D； PDBConstruct 1–509； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gk2
Deposition date deposition_date	2001-08-07
Structure title title	Histidine Ammonia-Lyase (HAL) Mutant F329G from Pseudomonas putida
Keywords keywords	LYASE, HISTIDINE DEGRADATION; LYASE
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	35.63 Å
Radius of gyration Rg (electron density) rg_electron	34.79 Å
Forward intensity I(0) i0	703698000.00
Molecular weight molecular_weight	214740.0 kDa
Excluded volume excluded_volume	268540 Å³
Envelope volume envelope_volume	310150 Å³
Hydration-shell volume shell_volume	68726 Å³
Envelope diameter envelope_diameter	110.3 Å
Shell Rg shell_rg	44.87 Å
Envelope Rg envelope_rg	35.03 Å
Shape Rg shape_rg	34.80 Å
Total Rg total_rg	35.36 Å
Total atoms total_atoms	15072
Residues n_residues	2036
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	106.9 Å
Rg (real space) rg_real	35.39 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	7.0370e+08
I(0) uncertainty (real space) i0_real_error	1.0210e+07
Rg (reciprocal space) rg_reciprocal	35.54 Å
I(0) (reciprocal space) i0_reciprocal	703800000.0000
Solution quality estimate total_estimate	0.9018
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.2 Å
Skewness Skewness skewness	0.094
Kurtosis Kurtosis kurtosis	-0.553
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	330400000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.918

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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	HISTIDINE AMMONIA-LYASE
Molecular weight formula_weight	53565.1 kDa
EC 编号 ec_number	4.3.1.3
Mutation mutation	YES
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	16235

TELTLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGFGLLASTRIASHDLENLQRSLVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVIDALIALVNAEVYPHIPLKGSVGASGDLAPLAHMSLVLLGEGKARYKGQWLSATEALAVAGLEPLTLAAKEGLALLNGTQASTAYALRGLFYAEDLYAAAIACGGLSVEAVLGSRSPFDARIHEARGQRGQIDTAACFRDLLGDSSEVSLSHKNADKVQDPYSLRCQPQVMGACLTQLRQAAEVLGIEANAVSDNPLVFAAEGDVISGGNGHAEPVAMAADNLALAIAEIGSLSERRISLMMDKHMSQLPPFLVENGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGVLAIEWLGACQGLDLRKGLKTSAKLEKARQALRSEVAHYDRDRFFAPDIEKAVELLAKGSLTGLLPAGVLPSL

来源 Source

来源生物 organism	PSEUDOMONAS PUTIDA
NCBI Class编号 ncbi_taxonomy_id	303
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1163

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1gk2a_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.2 — HAL/PAL-like

Domain ID domain_id	d1gk2b_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.2 — HAL/PAL-like

Domain ID domain_id	d1gk2c_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.2 — HAL/PAL-like

Domain ID domain_id	d1gk2d_
Class class	a — All alpha proteins
Fold Fold fold	a.127 — L-aspartase-like
Superfamily Superfamily superfamily	a.127.1 — L-aspartase-like
Family Family family	a.127.1.2 — HAL/PAL-like

CATH v4.4 (8 domains)

Domain ID domain_id	1gk2A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1gk2A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1gk2B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1gk2B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1gk2C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1gk2C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

Domain ID domain_id	1gk2D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	275 — Fumarase C; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (N-terminal domain)

Domain ID domain_id	1gk2D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	200 — Fumarase C; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Fumarase/aspartase (Central domain)

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8. Citations (3)

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Unit-cell length a length_a	77.966 Å
Unit-cell length b length_b	130.561 Å
Unit-cell length c length_c	115.835 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.00 °
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	1.900 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1700
R_work r_work	—
R_free r_free	0.2260

fit	/app/data/saxs_computation/gk/1gk2/1gk2.fit
pddf	/app/data/pr_computation/gk/1gk2/1gk2.pr.out
profile	/app/data/saxs_computation/gk/1gk2/1gk2.dat

Histidine Ammonia-Lyase (HAL) Mutant F329G from Pseudomonas putida

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

HISTIDINE AMMONIA-LYASE

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