SAXSdb — 1d9e

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

3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE

Escherichia coli

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 1–284 Chain B； UniProt 1–284 Chain C； UniProt 1–284 Chain D； UniProt 1–284	Not recorded	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；AMMONIUM SULFATE, POTASSIUM PHOSPHATE, ETHYLENE GLYCOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.239

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 1D9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G7U CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE Deposited 2000-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	PEP PHOSPHOENOLPYRUVATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；MES 61mM pH 6.1, Glycerol 25% v/v, PEG 400 10% v/v, 3mg/mL PEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.281
1G7U CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE Deposited 2000-11-14	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 A 1–284（284 aa）	Not recorded	PEP PHOSPHOENOLPYRUVATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；MES 61mM pH 6.1, Glycerol 25% v/v, PEG 400 10% v/v, 3mg/mL PEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.281
1G7V CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH THE MECHANISM-BASED INHIBITOR Deposited 2000-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	PAI {[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；MES or MOPS 61mM pH 6.1, 25% v/v Glycerol, 20mg/mL protein in tris buffer, 30 microgram/mL inhibitor, 10% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.242
1G7V CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH THE MECHANISM-BASED INHIBITOR Deposited 2000-11-14	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 A 1–284（284 aa）	Not recorded	PAI {[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；MES or MOPS 61mM pH 6.1, 25% v/v Glycerol, 20mg/mL protein in tris buffer, 30 microgram/mL inhibitor, 10% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.242
1GG0 CRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A Deposited 2000-08-04	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 1–284（284 aa）	Not recorded	PO4 PHOSPHATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；PEG 1500, 3-(N-morpholino)propanesulfonic acid, dithioerythitol, d-arabinose-5-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 3.00 Å R-free 0.265
1GG0 CRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A Deposited 2000-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–284（284 aa）	Not recorded	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；PEG 1500, 3-(N-morpholino)propanesulfonic acid, dithioerythitol, d-arabinose-5-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 3.00 Å R-free 0.265
1PHQ Crystal structure of KDO8P synthase in its binary complex with substrate analog E-FPEP Deposited 2003-05-29	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 1–284（284 aa）	Not recorded	FPE 3-FLUORO-2-(PHOSPHONOOXY)PROPANOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 4000, Glycrol, Tris-HCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293 K	Resolution 2.70 Å R-free 0.322
1PHW Crystal structure of KDO8P synthase in its binary complex with substrate analog 1-deoxy-A5P Deposited 2003-05-29	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 1–284（284 aa）	Not recorded	N ANY 5'-MONOPHOSPHATE NUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；PEG 6000, Glycrol, Tris-HCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294 K	Resolution 2.36 Å R-free 0.313
1PL9 Crystal structure of KDO8P synthase in its binary complex with substrate analog Z-FPEP Deposited 2003-06-08	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 1–284（284 aa）	Not recorded	FPE 3-FLUORO-2-(PHOSPHONOOXY)PROPANOIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；294 K；EG 4000, Glycrol, Tris-HCl , pH 7.4 , VAPOR DIFFUSION, HANGING DROP, temperature 294 K	Resolution 2.90 Å R-free 0.327
1Q3N Crystal structure of KDO8P synthase in its binary complex with substrate PEP Deposited 2003-07-31	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 1–284（284 aa）	Not recorded	PEP PHOSPHOENOLPYRUVATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 4000, Glycrol, Tris-HCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.268
1X6U KDO8P synthase in it's binary complex with the product KDO8P Deposited 2004-08-12	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 1–284（284 aa）	Not recorded	DO8 3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG4000, Glycerol, Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.280
1X8F Crystal Structure Of apo-Kdo8P Synthase Deposited 2004-08-18	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 1–284（284 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG4000, tris-HCl, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.255

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDSA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 1–284 Author chain B； PDBConstruct 1–284； UniProt 1–284 Author chain C； PDBConstruct 1–284； UniProt 1–284 Author chain D； PDBConstruct 1–284； UniProt 1–284

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	1d9e
Deposition date deposition_date	1999-10-27
Structure title title	STRUCTURE OF E. COLI KDO8P SYNTHASE
Keywords keywords	KDO, KDO8P, TIM BARREL, DAH7P, PEP, A5P, LYASE; 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	31.64 Å
Radius of gyration Rg (electron density) rg_electron	30.74 Å
Forward intensity I(0) i0	207296000.00
Molecular weight molecular_weight	116910.0 kDa
Excluded volume excluded_volume	147390 Å³
Envelope volume envelope_volume	175010 Å³
Hydration-shell volume shell_volume	45594 Å³
Envelope diameter envelope_diameter	100.0 Å
Shell Rg shell_rg	39.33 Å
Envelope Rg envelope_rg	30.39 Å
Shape Rg shape_rg	30.73 Å
Total Rg total_rg	31.49 Å
Total atoms total_atoms	8194
Residues n_residues	1062
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	94.9 Å
Rg (real space) rg_real	31.45 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	2.0730e+08
I(0) uncertainty (real space) i0_real_error	3.0910e+06
Rg (reciprocal space) rg_reciprocal	31.54 Å
I(0) (reciprocal space) i0_reciprocal	207300000.0000
Solution quality estimate total_estimate	0.7145
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.0 Å
Skewness Skewness skewness	0.115
Kurtosis Kurtosis kurtosis	-0.648
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	144000000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.992; Smooth: 0.885

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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	3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
Molecular weight formula_weight	30870.7 kDa
EC 编号 ec_number	4.1.2.16
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	8618

MKQKVVSIGDINVANDLPFVLFGGMNVLESRDLAMRICEHYVTVTQKLGIPYVFKASFDKANRSSIHSYRGPGLEEGMKIFQELKQTFGVKIITDVHEPSQAQPVADVVDVIQLPAFLARQTDLVEAMAKTGAVINVKKPQFVSPGQMGNIVDKFKEGGNEKVILCDRGANFGYDNLVVDMLGFSIMKKVSGNSPVIFDVTHALQCRDPFGAASGGRRAQVAELARAGMAVGLAGLFIEAHPDPEHAKCDGPSALPLAKLEPFLKQMKAIDDLVKGFEELDTSK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
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	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	424

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d9ea_
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.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1d9eb_
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.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1d9ec_
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.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1d9ed_
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.1.10.4 — Class I DAHP synthetase

CATH v4.4 (4 domains)

Domain ID domain_id	1d9eA00
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	1d9eB00
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	1d9eC00
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	1d9eD00
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	228.620 Å
Unit-cell length b length_b	228.620 Å
Unit-cell length c length_c	228.620 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	96

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	22.860 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2390

fit	/app/data/saxs_computation/d9/1d9e/1d9e.fit
pddf	/app/data/pr_computation/d9/1d9e/1d9e.pr.out
profile	/app/data/saxs_computation/d9/1d9e/1d9e.dat

STRUCTURE OF E. COLI KDO8P SYNTHASE

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

3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE 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