3hxa

Crystal Structure of DCoH1Thr51Ser

Method: X-RAY DIFFRACTION D_max: 112.8 Å Quality: GOOD

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

Pterin-4-alpha-carbinolamine dehydratase

Rattus norvegicus

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 1–104 Chain B； UniProt 1–104 Chain C； UniProt 1–104 Chain D； UniProt 1–104	Mutation：T51S	SO4 SULFATE ION × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：Hanging drop；pH 7.5；291 K；HEPES, Ammonium Sulfate, PEG 200, Glycerol, pH 7.5, Hanging drop, temperature 291K	Resolution 1.80 Å R-free 0.226
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–104 Chain F； UniProt 1–104 Chain G； UniProt 1–104 Chain H； UniProt 1–104	Mutation：T51S	SO4 SULFATE ION × 4 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions：Hanging drop；pH 7.5；291 K；HEPES, Ammonium Sulfate, PEG 200, Glycerol, pH 7.5, Hanging drop, temperature 291K	Resolution 1.80 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 3HXA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DCH CRYSTAL STRUCTURE OF DCOH, A BIFUNCTIONAL, PROTEIN-BINDING TRANSCRIPTION COACTIVATOR Deposited 1995-01-24	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 1–103（103 aa） Chain B 1–103（103 aa） Chain C 1–103（103 aa） Chain D 1–103（103 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2 COMPND ROOM TEMP., 1.7M AMSO4, .1M HEPES, PH 7.2.	Resolution 3.00 Å
1DCH CRYSTAL STRUCTURE OF DCOH, A BIFUNCTIONAL, PROTEIN-BINDING TRANSCRIPTION COACTIVATOR Deposited 1995-01-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–103（103 aa） Chain F 1–103（103 aa） Chain G 1–103（103 aa） Chain H 1–103（103 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2 COMPND ROOM TEMP., 1.7M AMSO4, .1M HEPES, PH 7.2.	Resolution 3.00 Å
1DCO DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR Deposited 1996-05-16	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 A 1–103（103 aa） Chain B 1–103（103 aa） Chain C 1–103（103 aa） Chain D 1–103（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4	Resolution 2.30 Å
1DCO DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR Deposited 1996-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–103（103 aa） Chain F 1–103（103 aa） Chain G 1–103（103 aa） Chain H 1–103（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4	Resolution 2.30 Å
1DCP DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR, COMPLEXED WITH BIOPTERIN Deposited 1996-05-16	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 A 1–103（103 aa） Chain B 1–103（103 aa） Chain C 1–103（103 aa） Chain D 1–103（103 aa）	Not recorded	HBI 7,8-DIHYDROBIOPTERIN × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4	Resolution 2.30 Å
1DCP DCOH, A BIFUNCTIONAL PROTEIN-BINDING TRANSCRIPTIONAL COACTIVATOR, COMPLEXED WITH BIOPTERIN Deposited 1996-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–103（103 aa） Chain F 1–103（103 aa） Chain G 1–103（103 aa） Chain H 1–103（103 aa）	Not recorded	HBI 7,8-DIHYDROBIOPTERIN × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；ROOM TEMPERATURE, 1.7M AMSO4, 0.1M HEPES, PH 7.4	Resolution 2.30 Å
1F93 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF HNF-1 ALPHA AND THE COACTIVATOR DCOH Deposited 2000-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；PEG 8000, potassium succinate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.60 Å R-free 0.299
1F93 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF HNF-1 ALPHA AND THE COACTIVATOR DCOH Deposited 2000-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–104（104 aa） Chain D 1–104（104 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；PEG 8000, potassium succinate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.60 Å R-free 0.299

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHS_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain B； PDBConstruct 1–104； UniProt 1–104 Author chain C； PDBConstruct 1–104； UniProt 1–104 Author chain D； PDBConstruct 1–104； UniProt 1–104 Author chain E； PDBConstruct 1–104； UniProt 1–104 Author chain F； PDBConstruct 1–104； UniProt 1–104 Author chain G； PDBConstruct 1–104； UniProt 1–104 Author chain H； PDBConstruct 1–104； UniProt 1–104

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3hxa
Deposition date deposition_date	2009-06-20
Structure title title	Crystal Structure of DCoH1Thr51Ser
Keywords keywords	alpha and beta structure, Lyase, Nucleus, Tetrahydrobiopterin biosynthesis; 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	34.96 Å
Radius of gyration Rg (electron density) rg_electron	34.34 Å
Forward intensity I(0) i0	133604000.00
Molecular weight molecular_weight	90593.0 kDa
Excluded volume excluded_volume	112330 Å³
Envelope volume envelope_volume	143780 Å³
Hydration-shell volume shell_volume	35771 Å³
Envelope diameter envelope_diameter	112.8 Å
Shell Rg shell_rg	39.68 Å
Envelope Rg envelope_rg	34.11 Å
Shape Rg shape_rg	34.31 Å
Total Rg total_rg	34.80 Å
Total atoms total_atoms	6393
Residues n_residues	796
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	112.8 Å
Rg (real space) rg_real	35.02 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.3360e+08
I(0) uncertainty (real space) i0_real_error	2.1060e+06
Rg (reciprocal space) rg_reciprocal	34.99 Å
I(0) (reciprocal space) i0_reciprocal	133600000.0000
Solution quality estimate total_estimate	0.8958
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.296
Kurtosis Kurtosis kurtosis	-0.697
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10350000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.942

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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	Pterin-4-alpha-carbinolamine dehydratase
Molecular weight formula_weight	12003.6 kDa
EC 编号 ec_number	4.2.1.96
Mutation mutation	T51S
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	7057

MAGKAHRLSAEERDQLLPNLRAVGWNELEGRDAIFKQFHFKDFNRAFGFMSRVALQAEKLDHHPEWFNVYNKVHITLSTHECAGLSERDINLASFIEQVAVSMT

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
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	8

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	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	524

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3hxaa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

Domain ID domain_id	d3hxab_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

Domain ID domain_id	d3hxac_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

Domain ID domain_id	d3hxad_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

Domain ID domain_id	d3hxae_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

Domain ID domain_id	d3hxaf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

Domain ID domain_id	d3hxag_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

Domain ID domain_id	d3hxah_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.1 — PCD-like
Family Family family	d.74.1.1 — PCD-like

CATH v4.4 (8 domains)

Domain ID domain_id	3hxaA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

Domain ID domain_id	3hxaB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

Domain ID domain_id	3hxaC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

Domain ID domain_id	3hxaD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

Domain ID domain_id	3hxaE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

Domain ID domain_id	3hxaF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

Domain ID domain_id	3hxaG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

Domain ID domain_id	3hxaH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	20 — Transcriptional coactivator/pterin dehydratase

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8. Citations (3)

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Unit-cell length a length_a	103.805 Å
Unit-cell length b length_b	103.805 Å
Unit-cell length c length_c	193.629 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2110
R_free r_free	0.2260

fit	/app/data/saxs_computation/hx/3hxa/3hxa.fit
pddf	/app/data/pr_computation/hx/3hxa/3hxa.pr.out
profile	/app/data/saxs_computation/hx/3hxa/3hxa.dat