SAXSdb — 1cbk

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

PROTEIN (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE)

Haemophilus influenzae

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 9–168 Chain B； UniProt 9–168	Not recorded	SO4 SULFATE ION × 2 ROI 7,8-DIHYDRO-7,7-DIMETHYL-6-HYDROXYPTERIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 2.02 Å R-free 0.213

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	HPPK_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–160； UniProt 9–168 Author chain B； PDBConstruct 1–160； UniProt 9–168

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	1cbk
Deposition date deposition_date	1999-02-26
Structure title title	7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE FROM HAEMOPHILUS INFLUENZAE
Keywords keywords	PYROPHOSPHOKINASE, 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	21.23 Å
Radius of gyration Rg (electron density) rg_electron	20.37 Å
Forward intensity I(0) i0	23120500.00
Molecular weight molecular_weight	37201.0 kDa
Excluded volume excluded_volume	46853 Å³
Envelope volume envelope_volume	55107 Å³
Hydration-shell volume shell_volume	22516 Å³
Envelope diameter envelope_diameter	67.9 Å
Shell Rg shell_rg	26.97 Å
Envelope Rg envelope_rg	20.33 Å
Shape Rg shape_rg	20.34 Å
Total Rg total_rg	21.34 Å
Total atoms total_atoms	2620
Residues n_residues	320
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	66.8 Å
Rg (real space) rg_real	21.16 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	2.3120e+07
I(0) uncertainty (real space) i0_real_error	2.7530e+05
Rg (reciprocal space) rg_reciprocal	21.18 Å
I(0) (reciprocal space) i0_reciprocal	23120000.0000
Solution quality estimate total_estimate	0.7512
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.5 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.296
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6416000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

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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	PROTEIN (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE)
Molecular weight formula_weight	18320.0 kDa
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	3024

MITAYIALGSNLNTPVEQLHAALKAISQLSNTHLVTTSSFYKSKPLGPQDQPDYVNAVAKIETELSPLKLLDELQRIENEQGRVRLRRWGERTLDLDILLYGNEIIQNERLTIPHYDMHNREFVIVPLFEIASDLVLPNSQIITELVKQFADHKMIKLNP

来源 Source

来源生物 organism	Haemophilus influenzae
NCBI Class编号 ncbi_taxonomy_id	727
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 non-polymer

Description description	7,8-DIHYDRO-7,7-DIMETHYL-6-HYDROXYPTERIN
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	404

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cbka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.30 — 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK
Family Family family	d.58.30.1 — 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK

Domain ID domain_id	d1cbkb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.30 — 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK
Family Family family	d.58.30.1 — 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK

CATH v4.4 (2 domains)

Domain ID domain_id	1cbkA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	560 — 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

Domain ID domain_id	1cbkB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	560 — 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK

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8. Citations (1)

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Unit-cell length a length_a	112.775 Å
Unit-cell length b length_b	50.791 Å
Unit-cell length c length_c	70.893 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.73 °
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	2.020 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1620
R_free r_free	0.2130

fit	/app/data/saxs_computation/cb/1cbk/1cbk.fit
pddf	/app/data/pr_computation/cb/1cbk/1cbk.pr.out
profile	/app/data/saxs_computation/cb/1cbk/1cbk.dat

7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE FROM HAEMOPHILUS INFLUENZAE

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

PROTEIN (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE)

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