SAXSdb — 1w5m

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

DELTA-AMINOLEVULINIC ACID DEHYDRATASE

PSEUDOMONAS AERUGINOSA

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–337 Chain B； UniProt 1–337	Mutation：YES	CL CHLORIDE ION × 8 FMT FORMIC ACID × 8 MG MAGNESIUM ION × 28 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (7.5 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM BETA-MERCAPTOETHANOLE) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (30.0 % (W/V) PEG 400, 100MM NA-HEPES PH 8.5, 200 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.	Resolution 1.60 Å R-free 0.165

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 1W5M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4K High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase Deposited 1998-12-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Not recorded	SO4 SULFATE ION × 8 MG MAGNESIUM ION × 4 SHF LAEVULINIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 1.67 Å R-free 0.208
1GZG Complex of a Mg2-dependent porphobilinogen synthase from Pseudomonas aeruginosa (mutant D139N) with 5-fluorolevulinic acid Deposited 2002-05-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Mutation：YES	LAF 5-FLUOROLEVULINIC ACID × 16 MG MAGNESIUM ION × 8 NA SODIUM ION × 8 SO4 SULFATE ION × 8 K POTASSIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；PROTEIN SOLUTION: 12 MG/ML PBGS MUTANT D139N IN 50 MM K-HEPES, 10 MM MGCL2. CRYSTALLIZATION SOLUTION: 0.99 ML PROTEIN SOLUTION = 0.01 ML 2MM 5F-LA IN 50 MM K-HEPES, 10 MM MGCL2. RESERVOIR SOLUTION: 1 M NA/K-TARTRATE, 0.2M LI2SO4, 0.1 M CHES PH = 9,5. SITTING DROP: 0.003 ML CRYSTALLISATION SOLUTION + 0.003 ML RESERVOIR SOLUTION	Resolution 1.66 Å R-free 0.198
1W54 Stepwise introduction of a zinc binding site into Porphobilinogen synthase from Pseudomonas aeruginosa (mutation D139C) Deposited 2004-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Mutation：YES	FMT FORMIC ACID × 8 K POTASSIUM ION × 8 MG MAGNESIUM ION × 8 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION (28,5 % (W/V) PEG-400, 100 MM NA-HEPES PH 7.5, 80MM MGCL2, 20MM DTT) ABOVE 500 MICROL OF RESERVOIR SOLUTION.	Resolution 2.20 Å R-free 0.217
1W56 Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C and D131C) Deposited 2004-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Mutation：YES	FMT FORMIC ACID × 8 MG MAGNESIUM ION × 12 ZN ZINC ION × 8 K POTASSIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (9 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (31.5 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 20 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES,HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.	Resolution 1.70 Å R-free 0.182
1W5N Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations D131C and D139C) Deposited 2004-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Mutation：YES	FMT FORMIC ACID × 8 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 12 ZN ZINC ION × 8 NA SODIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (9 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM BETA-MERCAPTOETHANOLE) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (30.0 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 40 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.	Resolution 1.65 Å R-free 0.188
1W5O Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, D131C and D139C) Deposited 2004-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Mutation：YES	GOL GLYCEROL × 8 K POTASSIUM ION × 8 MG MAGNESIUM ION × 8 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；SITTING DROP. DROPS WERE MIXED OF 3 MICROLITER OF PROTEIN SOLUTION (7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 3 MICROLITER OF RESERVOIR SOLUTION (1M K/NA-TARTRATE, 100MM MES PH 6.0, 20MM BETA-MERCAPTOETHANOLE), 100 MICROLITER OF RESERVOIR SOLUTION, 96 WELL PLATES (NUNC)	Resolution 1.85 Å R-free 0.176
1W5P Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, D131C, D139C, P132E) Deposited 2004-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Mutation：YES	EDO 1,2-ETHANEDIOL × 20 FMT FORMIC ACID × 8 K POTASSIUM ION × 8 MG MAGNESIUM ION × 8 SO4 SULFATE ION × 8 GOL GLYCEROL × 24 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；SITTING DROP. DROPS WERE MIXED OF 3 MICROLITER OF PROTEIN SOLUTION (12 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 1MM ZNCL2, 10 MM DTT) PLUS 3 MICROLITER OF RESERVOIR SOLUTION (1M LITHIUM SULFATE, 100MM TRIS-HCL PH 8.5, 10MM NICKEL CHLORIDE), 100 MICROLITER OF RESERVOIR SOLUTION, 96 WELL PLATES (NUNC) IN AN ANAEROBIC BOX	Resolution 1.55 Å R-free 0.185
1W5Q Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, D131C, D139C, P132E, K229R) Deposited 2004-08-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Mutation：YES	FMT FORMIC ACID × 8 MG MAGNESIUM ION × 20 ZN ZINC ION × 8 NA SODIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (10 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 MICROM ZNCL2, 10 MM DTT) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (30.0 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 80 MM MGCL2, 20MM DTT) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION, IN AN ANAEROBIC BOX.	Resolution 1.40 Å R-free 0.173
2C13 5-hydroxy-levulinic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa Deposited 2005-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CL CHLORIDE ION × 8 PEG DI(HYDROXYETHYL)ETHER × 4 K POTASSIUM ION × 8 PGE TRIETHYLENE GLYCOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP IN 24-WELL LIMBRO PLATES.DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.05 M TRIS-HCL, PH 7.5, 0.005 M MGCL2, 0.01 M 5-OH-4-OXO-PENTANOIC ACID SODIUM SALT PLUS 5 MICROL RESERVOIR SOLUTION 9.0 % (W/V) PEG-4000, 0.180 M KCL, 0.009 M CACL2, 0.05 M NA-CACODYLATE PH 6.0	Resolution 2.15 Å R-free 0.204
2C14 5-(4-Carboxy-2-oxo-butylamino)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa Deposited 2005-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 1MM NACL, 1 MM 5-(4-CARBOXY-2-OXO-BUTYLAMINO)-4-OXO-PENTANOIC ACID MONOSODIUM SALT)) PLUS 5 MICROL RESERVOIR SOLUTION (18.0 % (W/V) PEG-3350, 200 MM LINO3)	Resolution 1.90 Å R-free 0.201
2C15 5-(4-Carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa Deposited 2005-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 100 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 5 MM 5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO-PENTANOIC ACID SODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (12.0 % (W/V) PEG-8000, 340 MM LI2SO4, 20% (V/V) GLYCEROL,)ABOVE 500 MICROL OF RESERVOIR SOLUTION.	Resolution 1.48 Å R-free 0.171
2C16 5-(4-Carboxy-2-oxo-butane-1-sulfinyl)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa Deposited 2005-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 PGE TRIETHYLENE GLYCOL × 8 PEG DI(HYDROXYETHYL)ETHER × 12 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 10 MM 5-(4-CARBOXY-2-OXO-BUTANE-1-SULFINYL)-4-OXO-PENTANOIC ACID DISODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (18.0 % (W/V) PEG-3350, 220 MM LICL) ABOVE 500 MICROL OF RESERVOIR SOLUTION.	Resolution 2.02 Å R-free 0.183
2C18 5-(4-Carboxy-2-oxo-butane-1-sulfonyl)-4-oxo-pentanoic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa Deposited 2005-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 28 NA SODIUM ION × 8 CL CHLORIDE ION × 8 PGE TRIETHYLENE GLYCOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROLITRES PROTEIN SOLUTION, 10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 10 MM 5-(4-CARBOXY-2-OXO-BUTANE-1-SULFONYL)-4-OXO-PENTANOIC ACID DISODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (31.0 % (V/V) PEG-400, 100 MM NA-HEPES PH 7.5, 180 MM MGCL2) ABOVE 500 MICROL OF RESERVOIR SOLUTION.	Resolution 1.93 Å R-free 0.186
2C19 5-(4-Carboxy-2-oxo-butylsulfanyl)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa Deposited 2005-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa） Chain B 1–337（337 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 NA SODIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 10 MM 5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO-PENTANOIC ACID DISODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (17.0 % (W/V) PEG-3350, 120 MM NA-TARTRATE) ABOVE 500 MICROL OF RESERVOIR SOLUTION.	Resolution 2.05 Å R-free 0.201
2WOQ Porphobilinogen Synthase (HemB) in Complex with 5-acetamido-4- oxohexanoic acid (Alaremycin 2) Deposited 2009-07-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–337（337 aa）	Not recorded	AYC ALAREMYCIN 2 × 8 MG MAGNESIUM ION × 32 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 16 PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 32	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；100 MM HEPES PH 7.5, 200 MM MGCL2, 30 % PEG400 TEMPERATURE = 17 C PROTEIN CONCENTRATION = 20 MG/ML	Resolution 1.75 Å R-free 0.180

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HEM2_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–337； UniProt 1–337 Author chain B； PDBConstruct 1–337； UniProt 1–337

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	1w5m
Deposition date deposition_date	2004-08-09
Structure title title	Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C and D139C)
Keywords keywords	SYNTHASE, EVOLUTION, METALLOENZYME, PORPHOBILINOGEN SYNTHASE, PSEUDOMONAS AERUGINOSA, PROTEIN ENGINEERING; SYNTHASE
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	27.06 Å
Radius of gyration Rg (electron density) rg_electron	25.99 Å
Forward intensity I(0) i0	88744200.00
Molecular weight molecular_weight	72270.0 kDa
Excluded volume excluded_volume	89790 Å³
Envelope volume envelope_volume	103890 Å³
Hydration-shell volume shell_volume	33005 Å³
Envelope diameter envelope_diameter	87.0 Å
Shell Rg shell_rg	34.01 Å
Envelope Rg envelope_rg	26.18 Å
Shape Rg shape_rg	26.01 Å
Total Rg total_rg	26.73 Å
Total atoms total_atoms	5068
Residues n_residues	654
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	86.0 Å
Rg (real space) rg_real	27.04 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	8.8740e+07
I(0) uncertainty (real space) i0_real_error	1.2510e+06
Rg (reciprocal space) rg_reciprocal	27.05 Å
I(0) (reciprocal space) i0_reciprocal	88740000.0000
Solution quality estimate total_estimate	0.8920
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.344
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24980000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.914

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DELTA-AMINOLEVULINIC ACID DEHYDRATASE
Molecular weight formula_weight	37084.0 kDa
EC 编号 ec_number	4.2.1.24
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6446

MSFTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVCLDPFTTHGQCGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR

来源 Source

来源生物 organism	PSEUDOMONAS AERUGINOSA
NCBI Class编号 ncbi_taxonomy_id	208964
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	887

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1w5ma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.3 — 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)

Domain ID domain_id	d1w5mb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.3 — 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)

CATH v4.4 (2 domains)

Domain ID domain_id	1w5mA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1w5mB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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8. Citations (1)

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Unit-cell length a length_a	126.307 Å
Unit-cell length b length_b	126.307 Å
Unit-cell length c length_c	85.156 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	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	87.710 Å
R factor r_factor	0.1310
R_work r_work	0.1290
R_free r_free	0.1650

fit	/app/data/saxs_computation/w5/1w5m/1w5m.fit
pddf	/app/data/pr_computation/w5/1w5m/1w5m.pr.out
profile	/app/data/saxs_computation/w5/1w5m/1w5m.dat

Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C and D139C)