SAXSdb — 3hyb

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

RbcX protein

Anabaena sp.

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 1–135 Chain B； UniProt 1–135	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；1 M (NH4)2SO4, 0.1 M Bis-Tris-HCl pH 5.5, 1 % PEG-3350, vapor diffusion, sitting drop, temperature 291K	Resolution 2.30 Å R-free 0.275

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 3HYB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PEO Crystal structure of RbcX from Anabaena CA Deposited 2007-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–135（135 aa） Chain B 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；1.0 M Ammonium phosphate, 0.1 M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.298
2WVW Cryo-EM structure of the RbcL-RbcX complex Deposited 2009-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain I 1–135（135 aa） Chain J 1–135（135 aa） Chain K 1–135（135 aa） Chain L 1–135（135 aa） Chain M 1–135（135 aa） Chain N 1–135（135 aa） Chain O 1–135（135 aa） Chain P 1–135（135 aa） Chain Q 1–135（135 aa） Chain R 1–135（135 aa） Chain S 1–135（135 aa） Chain T 1–135（135 aa） Chain U 1–135（135 aa） Chain V 1–135（135 aa） Chain W 1–135（135 aa） Chain X 1–135（135 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 MM TRIS-HCL, PH 8.7；pH 8.7；20 MM TRIS-HCL, PH 8.7 cryo-EM vitrification conditions Cryogen ETHANE；VITROBOT USED, LIQUID ETHANE	Resolution 9.00 Å
3RG6 Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco Deposited 2011-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain C 1–135（135 aa） Chain D 1–135（135 aa） Chain E 1–135（135 aa） Chain F 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；277 K；15-17 % 2-methyl-2,4-pentanediol, 0.1 M KCl, 0.1 M Tris-HCl, pH 8.7, vapor diffusion, temperature 277K	Resolution 3.20 Å R-free 0.245

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q44212_9NOST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–155； UniProt 1–135 Author chain B； PDBConstruct 21–155； UniProt 1–135

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	3hyb
Deposition date deposition_date	2009-06-22
Structure title title	Crystal structure of RbcX from Anabaena, crystal form II
Keywords keywords	RuBisCO, protein complex assembly, chaperone; CHAPERONE
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	20.97 Å
Radius of gyration Rg (electron density) rg_electron	20.36 Å
Forward intensity I(0) i0	11106400.00
Molecular weight molecular_weight	25206.0 kDa
Excluded volume excluded_volume	31733 Å³
Envelope volume envelope_volume	38597 Å³
Hydration-shell volume shell_volume	16581 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	25.79 Å
Envelope Rg envelope_rg	20.98 Å
Shape Rg shape_rg	20.36 Å
Total Rg total_rg	21.15 Å
Total atoms total_atoms	1773
Residues n_residues	230
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	84.1 Å
Rg (real space) rg_real	21.05 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	1.1110e+07
I(0) uncertainty (real space) i0_real_error	1.7740e+05
Rg (reciprocal space) rg_reciprocal	21.04 Å
I(0) (reciprocal space) i0_reciprocal	11110000.0000
Solution quality estimate total_estimate	0.7668
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.451
Kurtosis Kurtosis kurtosis	-0.159
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2994000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.484; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.512; Smooth: 0.999

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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	RbcX protein
Molecular weight formula_weight	17694.9 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	1887

MGSSHHHHHHSSGLVPRGSHMNLKQIAKDTAKTLQSYLTYQALRTVLAQLGETNPPLALWLHNFSAGKVQDGEKYIEELFLEKPDLALRIMTVREHIAEEIAEFLPEMVVTGIQQANMEKRRQHLERMTQVSLSHPSPESEQQQFSDPDWDNLAS

来源 Source

来源生物 organism	Anabaena sp.
NCBI Class编号 ncbi_taxonomy_id	1167
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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3hyba1
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d3hyba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3hybb1
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d3hybb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3hybA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	3hybB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

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8. Citations (1)

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Unit-cell length a length_a	74.990 Å
Unit-cell length b length_b	74.990 Å
Unit-cell length c length_c	123.841 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2470
R_work r_work	0.2460
R_free r_free	0.2750

fit	/app/data/saxs_computation/hy/3hyb/3hyb.fit
pddf	/app/data/pr_computation/hy/3hyb/3hyb.pr.out
profile	/app/data/saxs_computation/hy/3hyb/3hyb.dat

Crystal structure of RbcX from Anabaena, crystal form II

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

RbcX protein

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