SAXSdb — 1b8f

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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	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

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 1B8F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EB4 Histidine Ammonia-Lyase (HAL) Mutant F329A from Pseudomonas putida Deposited 2001-07-19	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
1GK2 Histidine Ammonia-Lyase (HAL) Mutant F329G from Pseudomonas putida Deposited 2001-08-07	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） 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 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 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；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 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 1–507； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b8f
Deposition date deposition_date	1999-01-31
Structure title title	Histidine ammonia-lyase (HAL) from Pseudomonas putida
Keywords keywords	AMMONIA-LYASE, HISTIDINE DEGRADATION, LYASE; 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	27.27 Å
Radius of gyration Rg (electron density) rg_electron	26.63 Å
Forward intensity I(0) i0	48298900.00
Molecular weight molecular_weight	53741.0 kDa
Excluded volume excluded_volume	67247 Å³
Envelope volume envelope_volume	80122 Å³
Hydration-shell volume shell_volume	26159 Å³
Envelope diameter envelope_diameter	97.1 Å
Shell Rg shell_rg	32.57 Å
Envelope Rg envelope_rg	27.06 Å
Shape Rg shape_rg	26.63 Å
Total Rg total_rg	27.25 Å
Total atoms total_atoms	3773
Residues n_residues	506
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	93.5 Å
Rg (real space) rg_real	27.49 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	4.8300e+07
I(0) uncertainty (real space) i0_real_error	7.5700e+05
Rg (reciprocal space) rg_reciprocal	27.42 Å
I(0) (reciprocal space) i0_reciprocal	48300000.0000
Solution quality estimate total_estimate	0.8482
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.520
Kurtosis Kurtosis kurtosis	-0.309
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11850000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.854; Smooth: 0.937

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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	53619.2 kDa
EC 编号 ec_number	4.3.1.3
Mutation mutation	C273A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3983

TELTLKPGTLTLAQLRAIHAAPVRLQLDASAAPAIDASVACVEQIIAEDRTAYGINTGFGLLASTRIASHDLENLQRSLVLSHAAGIGAPLDDDLVRLIMVLKINSLSRGFSGIRRKVIDALIALVNAEVYPHIPLKGSVGXDLAPLAHMSLVLLGEGKARYKGQWLSATEALAVAGLEPLTLAAKEGLALLNGTQASTAYALRGLFYAEDLYAAAIACGGLSVEAVLGSRSPFDARIHEARGQRGQIDTAACFRDLLGDSSEVSLSHKNADKVQDPYSLRCQPQVMGACLTQLRQAAEVLGIEANAVSDNPLVFAAEGDVISGGNFHAEPVAMAADNLALAIAEIGSLSERRISLMMDKHMSQLPPFLVENGGVNSGFMIAQVTAAALASENKALSHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTRGVLAIEWLGACQGLDLRKGLKTSAKLEKARQALRSEVAHYDRDRFFAPDIEKAVELLAKGSLTGLLPAGVLPSL

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

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	210

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b8fa_
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 (2 domains)

Domain ID domain_id	1b8fA01
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	1b8fA02
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 (2)

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Unit-cell length a length_a	79.267 Å
Unit-cell length b length_b	116.788 Å
Unit-cell length c length_c	129.532 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	39.000 Å
R factor r_factor	0.1970
R_work r_work	0.1870
R_free r_free	0.2630

fit	/app/data/saxs_computation/b8/1b8f/1b8f.fit
pddf	/app/data/pr_computation/b8/1b8f/1b8f.pr.out
profile	/app/data/saxs_computation/b8/1b8f/1b8f.dat

Histidine ammonia-lyase (HAL) 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