SAXSdb — 1f28

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

THYMIDYLATE SYNTHASE

Pneumocystis carinii

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–297 Chain B； UniProt 1–297	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 F89 S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；297 K；PEG 8000, Tris, Ammonium sulfate, DTT, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 24K	Resolution 1.90 Å R-free 0.247
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–297 Chain D； UniProt 1–297	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 F89 S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；297 K；PEG 8000, Tris, Ammonium sulfate, DTT, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 24K	Resolution 1.90 Å R-free 0.247

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 1F28	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CI7 TERNARY COMPLEX OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII Deposited 1999-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–297（297 aa） Chain B 1–297（297 aa）	Not recorded	UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE × 2 CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；100 UM ENZYME, 2 MM DUMP, 2 MM CB3717, 1 MM DTT OVER 14.5 % PEG 8000, 0.25 M ( NH4)2SO4, 5 MM DTT, 0.1 M TRIS, PH 7.4	Resolution 2.60 Å R-free 0.294

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TYSY_PNECA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 1–297 Author chain B； PDBConstruct 1–297； UniProt 1–297 Author chain C； PDBConstruct 1–297； UniProt 1–297 Author chain D； PDBConstruct 1–297； UniProt 1–297

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	1f28
Deposition date deposition_date	2000-05-23
Structure title title	CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII BOUND TO DUMP AND BW1843U89
Keywords keywords	beta-sheet, protein-inhibitor complex, TRANSFERASE; TRANSFERASE
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	34.36 Å
Radius of gyration Rg (electron density) rg_electron	33.49 Å
Forward intensity I(0) i0	300471000.00
Molecular weight molecular_weight	139480.0 kDa
Excluded volume excluded_volume	174120 Å³
Envelope volume envelope_volume	212280 Å³
Hydration-shell volume shell_volume	51759 Å³
Envelope diameter envelope_diameter	114.5 Å
Shell Rg shell_rg	41.36 Å
Envelope Rg envelope_rg	33.23 Å
Shape Rg shape_rg	33.48 Å
Total Rg total_rg	34.05 Å
Total atoms total_atoms	9822
Residues n_residues	1180
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	109.8 Å
Rg (real space) rg_real	34.31 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	3.0050e+08
I(0) uncertainty (real space) i0_real_error	4.7040e+06
Rg (reciprocal space) rg_reciprocal	34.34 Å
I(0) (reciprocal space) i0_reciprocal	300500000.0000
Solution quality estimate total_estimate	0.8869
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.2 Å
Skewness Skewness skewness	0.311
Kurtosis Kurtosis kurtosis	-0.457
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	74010000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.798

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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	THYMIDYLATE SYNTHASE
Molecular weight formula_weight	34403.3 kDa
EC 编号 ec_number	2.1.1.45
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	10322

MVNAEEQQYLNLVQYIINHGEDRPDRTGTGTLSVFAPSPLKFSLRNKTFPLLTTKRVFIRGVIEELLWFIRGETDSLKLREKNIHIWDANGSREYLDSIGLTKRQEGDLGPIYGFQWRHFGAEYIDCKTNYIGQGVDQLANIIQKIRTSPYDRRLILSAWNPADLEKMALPPCHMFCQFYVHIPSNNHRPELSCQLYQRSCDMGLGVPFNIASYALLTCMIAHVCDLDPGDFIHVMGDCHIYKDHIEALQQQLTRSPRPFPTLSLNRSITDIEDFTLDDFNIQNYHPYETIKMKMSI

来源 Source

来源生物 organism	Pneumocystis carinii
NCBI Class编号 ncbi_taxonomy_id	4754
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
Molecular weight formula_weight	308.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID
Molecular weight formula_weight	500.5 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	500

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1f28a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

Domain ID domain_id	d1f28b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

Domain ID domain_id	d1f28c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

Domain ID domain_id	d1f28d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (4 domains)

Domain ID domain_id	1f28A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

Domain ID domain_id	1f28B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

Domain ID domain_id	1f28C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

Domain ID domain_id	1f28D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

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8. Citations (1)

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Unit-cell length a length_a	54.442 Å
Unit-cell length b length_b	65.898 Å
Unit-cell length c length_c	184.938 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.24 °
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	22.400 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2470

fit	/app/data/saxs_computation/f2/1f28/1f28.fit
pddf	/app/data/pr_computation/f2/1f28/1f28.pr.out
profile	/app/data/saxs_computation/f2/1f28/1f28.dat

CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS CARINII BOUND TO DUMP AND BW1843U89

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

THYMIDYLATE SYNTHASE

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