SAXSdb — 5bs1

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

CrRbcX-IIa

Chlamydomonas reinhardtii

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 35–155 Chain B； UniProt 35–155	Fragment：UNP residues 35-155 Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；5 % PEG-3350, 0.2 M MgCl2, 50 mM Tris-HCl pH 8.0	Resolution 1.60 Å R-free 0.206
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 35–155 Chain D； UniProt 35–155	Fragment：UNP residues 35-155 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；5 % PEG-3350, 0.2 M MgCl2, 50 mM Tris-HCl pH 8.0	Resolution 1.60 Å R-free 0.206

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 5BS1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5BS2 Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in complex with RbcL C-terminal tail Deposited 2015-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 44–156（113 aa） Fragment：UNP residues 462-473,UNP residues 44-156 Chain B 44–156（113 aa） Fragment：UNP residues 462-473,UNP residues 44-156	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Tris-HCl pH 8.5, 25% PEG2000 MME	Resolution 1.97 Å R-free 0.222

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

View Construct and Data Evidence

UniProt name	A8HQH2_CHLRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–122； UniProt 35–155 Author chain B； PDBConstruct 2–122； UniProt 35–155 Author chain C； PDBConstruct 2–122； UniProt 35–155 Author chain D； PDBConstruct 2–122； UniProt 35–155

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	5bs1
Deposition date deposition_date	2015-06-01
Structure title title	Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii
Keywords keywords	RbcX, 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	27.62 Å
Radius of gyration Rg (electron density) rg_electron	27.09 Å
Forward intensity I(0) i0	56376100.00
Molecular weight molecular_weight	54183.0 kDa
Excluded volume excluded_volume	65292 Å³
Envelope volume envelope_volume	82142 Å³
Hydration-shell volume shell_volume	26585 Å³
Envelope diameter envelope_diameter	102.2 Å
Shell Rg shell_rg	32.82 Å
Envelope Rg envelope_rg	27.50 Å
Shape Rg shape_rg	27.03 Å
Total Rg total_rg	27.79 Å
Total atoms total_atoms	3659
Residues n_residues	433
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	95.7 Å
Rg (real space) rg_real	27.79 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	5.6380e+07
I(0) uncertainty (real space) i0_real_error	8.1710e+05
Rg (reciprocal space) rg_reciprocal	27.74 Å
I(0) (reciprocal space) i0_reciprocal	56370000.0000
Solution quality estimate total_estimate	0.8443
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.2 Å
Skewness Skewness skewness	0.482
Kurtosis Kurtosis kurtosis	-0.216
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6964000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.668

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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	CrRbcX-IIa
Molecular weight formula_weight	14214.7 kDa
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	4185

MHIPADSFSGASPERKAAVALRSLFTFVAARVVLEQLQGPGGPETTYNQQAYLDLMDFLGTPMKGDGGDEWMAAVMRKNHALALRLMEVREAYLDEFEWGKTMEMASRETREANTRLMRAAAM

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI Class编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	388

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5bs1a1
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.280.1.0 — automated matches

Domain ID domain_id	d5bs1a2
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	d5bs1b1
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.280.1.0 — automated matches

Domain ID domain_id	d5bs1b2
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	d5bs1c_
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.280.1.0 — automated matches

Domain ID domain_id	d5bs1d_
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.280.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5bs1A00
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	5bs1B00
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	5bs1C00
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	5bs1D00
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	36.133 Å
Unit-cell length b length_b	52.989 Å
Unit-cell length c length_c	61.561 Å
Unit-cell angle α angle_alpha	76.49 °
Unit-cell angle β angle_beta	81.10 °
Unit-cell angle γ angle_gamma	70.10 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1787
R_work r_work	0.1772
R_free r_free	0.2060

fit	/app/data/saxs_computation/bs/5bs1/5bs1.fit
pddf	/app/data/pr_computation/bs/5bs1/5bs1.pr.out
profile	/app/data/saxs_computation/bs/5bs1/5bs1.dat

Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii

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

CrRbcX-IIa

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