SAXSdb — 1cz3

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

DIHYDROFOLATE REDUCTASE

Thermotoga maritima

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 2–169 Chain B； UniProt 2–169	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2 M (NH4)2SO4 25 MM TRIS/HCL 0.5 MM EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.255

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 1CZ3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D1G DIHYDROFOLATE REDUCTASE FROM THERMOTOGA MARITIMA Deposited 1999-09-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–169（168 aa） Chain B 2–169（168 aa）	Not recorded	NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MTX METHOTREXATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；10% PEG 3000, 33 MM TRIS/HCL, 1 MM MGSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.242

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

View Construct and Data Evidence

UniProt name	DYR_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 2–169 Author chain B； PDBConstruct 1–168； UniProt 2–169

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	1cz3
Deposition date deposition_date	1999-09-01
Structure title title	DIHYDROFOLATE REDUCTASE FROM THERMOTOGA MARITIMA
Keywords keywords	DIMER, HYPERTHERMOPHILE, oxidoreductase; OXIDOREDUCTASE
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	22.94 Å
Radius of gyration Rg (electron density) rg_electron	21.82 Å
Forward intensity I(0) i0	22737700.00
Molecular weight molecular_weight	38145.0 kDa
Excluded volume excluded_volume	48624 Å³
Envelope volume envelope_volume	57713 Å³
Hydration-shell volume shell_volume	22682 Å³
Envelope diameter envelope_diameter	83.1 Å
Shell Rg shell_rg	28.17 Å
Envelope Rg envelope_rg	22.12 Å
Shape Rg shape_rg	21.81 Å
Total Rg total_rg	22.76 Å
Total atoms total_atoms	2695
Residues n_residues	332
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	77.3 Å
Rg (real space) rg_real	22.99 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	2.2740e+07
I(0) uncertainty (real space) i0_real_error	3.0320e+05
Rg (reciprocal space) rg_reciprocal	22.98 Å
I(0) (reciprocal space) i0_reciprocal	22740000.0000
Solution quality estimate total_estimate	0.7844
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.474
Kurtosis Kurtosis kurtosis	-0.123
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7157000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DIHYDROFOLATE REDUCTASE
Molecular weight formula_weight	19263.3 kDa
EC 编号 ec_number	1.5.1.3
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	2899

AKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVEKSHR

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cz3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.1 — Dihydrofolate reductases

Domain ID domain_id	d1cz3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.1 — Dihydrofolate reductases

CATH v4.4 (2 domains)

Domain ID domain_id	1cz3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	1cz3B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

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8. Citations (1)

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Unit-cell length a length_a	131.605 Å
Unit-cell length b length_b	36.051 Å
Unit-cell length c length_c	97.025 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	130.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	9.010 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2550

fit	/app/data/saxs_computation/cz/1cz3/1cz3.fit
pddf	/app/data/pr_computation/cz/1cz3/1cz3.pr.out
profile	/app/data/saxs_computation/cz/1cz3/1cz3.dat

DIHYDROFOLATE REDUCTASE FROM THERMOTOGA MARITIMA

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

DIHYDROFOLATE REDUCTASE

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