SAXSdb — 1d8w

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

L-RHAMNOSE ISOMERASE

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 1–419 Chain B； UniProt 1–419 Chain C； UniProt 1–419 Chain D； UniProt 1–419	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；0.2 M CITRATE, 22.5-30% PEG 8000, 10% ISOPROPANOLE, 0.1 M HEPES, PH = 6.4 - 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.60 Å R-free 0.241

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 1D8W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DE5 L-RHAMNOSE ISOMERASE Deposited 1999-11-12	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 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa）	Not recorded	RNT L-RHAMNITOL × 4 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；0.2 M CITRATE, 0.1-M HEPES, 22.5 - 30.0 % PEG 8000, 10 % ISOPROPANOL, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.275
1DE6 L-RHAMNOSE ISOMERASE Deposited 1999-11-13	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 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa）	Not recorded	RNS L-RHAMNOSE × 4 ZN ZINC ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.2 M CITRATE, 0.1-M HEPES, 22.5 - 30.0 % PEG 8000, 10 % ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.10 Å R-free 0.244

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RHAA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–426； UniProt 1–419 Author chain B； PDBConstruct 8–426； UniProt 1–419 Author chain C； PDBConstruct 8–426； UniProt 1–419 Author chain D； PDBConstruct 8–426； UniProt 1–419

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	1d8w
Deposition date deposition_date	1999-10-26
Structure title title	L-RHAMNOSE ISOMERASE
Keywords keywords	BETA-ALPHA-8-BARRELS, ALDOSE-KETOSE ISOMERIZATION, HYDRIDE SHIFT, ISOMERASE; ISOMERASE
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	34.21 Å
Radius of gyration Rg (electron density) rg_electron	33.22 Å
Forward intensity I(0) i0	539047000.00
Molecular weight molecular_weight	184320.0 kDa
Excluded volume excluded_volume	228190 Å³
Envelope volume envelope_volume	265880 Å³
Hydration-shell volume shell_volume	62491 Å³
Envelope diameter envelope_diameter	105.0 Å
Shell Rg shell_rg	43.17 Å
Envelope Rg envelope_rg	33.03 Å
Shape Rg shape_rg	33.23 Å
Total Rg total_rg	33.81 Å
Total atoms total_atoms	12878
Residues n_residues	1575
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	100.8 Å
Rg (real space) rg_real	33.96 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	5.3900e+08
I(0) uncertainty (real space) i0_real_error	7.9350e+06
Rg (reciprocal space) rg_reciprocal	34.12 Å
I(0) (reciprocal space) i0_reciprocal	539100000.0000
Solution quality estimate total_estimate	0.9043
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.0 Å
Skewness Skewness skewness	0.020
Kurtosis Kurtosis kurtosis	-0.575
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	154900000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.943

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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	L-RHAMNOSE ISOMERASE
Molecular weight formula_weight	48592.4 kDa
EC 编号 ec_number	5.3.1.14
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	14687

GHHHHHHMTTQLEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQATGNYPGKARNASELRADLEQAMRLIPGPKRLNLHAIYLESDTPVSRDQIKPEHFKNWVEWAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLGTPSVMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESYTVGSNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVLLDDETQAIASEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAELRKLEAPGDYTARLALLEEQKSLPWQAVWEMYCQRHDTPAGSEWLESVRAYEKEILSRRG

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1809

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d8wa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.2 — L-rhamnose isomerase

Domain ID domain_id	d1d8wb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.2 — L-rhamnose isomerase

Domain ID domain_id	d1d8wc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.2 — L-rhamnose isomerase

Domain ID domain_id	d1d8wd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.2 — L-rhamnose isomerase

CATH v4.4 (4 domains)

Domain ID domain_id	1d8wA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	1d8wB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	1d8wC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	1d8wD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

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8. Citations (1)

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Unit-cell length a length_a	169.849 Å
Unit-cell length b length_b	163.104 Å
Unit-cell length c length_c	78.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1780
R_work r_work	0.1740
R_free r_free	0.2410

fit	/app/data/saxs_computation/d8/1d8w/1d8w.fit
pddf	/app/data/pr_computation/d8/1d8w/1d8w.pr.out
profile	/app/data/saxs_computation/d8/1d8w/1d8w.dat

L-RHAMNOSE ISOMERASE

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

L-RHAMNOSE ISOMERASE

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)