SAXSdb — 3eir

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

Putative ATP/GTP binding protein

Burkholderia pseudomallei

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 48–328	Fragment：residues 48-328 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 6；293 K；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.254
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 48–328	Fragment：residues 48-328 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 6；293 K；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.254

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 3EIR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EIT the 2.6 angstrom crystal structure of CHBP, the Cif Homologue from Burkholderia pseudomallei Deposited 2008-09-17	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 48–328（281 aa） Fragment：residues 48-328	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.56 Å R-free 0.267
3EIT the 2.6 angstrom crystal structure of CHBP, the Cif Homologue from Burkholderia pseudomallei Deposited 2008-09-17	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 48–328（281 aa） Fragment：residues 48-328	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.56 Å R-free 0.267
3GQM Crystal structure of Cell Inhibiting Factor (Cif) from Burkholderia pseudomallei (CifBp) Deposited 2009-03-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 67–328（262 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 % (w/v) PEG 8000, 100 mM HEPES 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.10 Å R-free 0.259
3GQM Crystal structure of Cell Inhibiting Factor (Cif) from Burkholderia pseudomallei (CifBp) Deposited 2009-03-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 67–328（262 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 % (w/v) PEG 8000, 100 mM HEPES 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.10 Å R-free 0.259
4HCN Crystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin Deposited 2012-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 78–328（251 aa） Fragment：unp RESIDUES 78-328	Mutation：A156C	PEG DI(HYDROXYETHYL)ETHER × 1 FMT FORMIC ACID × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.2；293 K；12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K	Resolution 2.60 Å R-free 0.260
4HCP crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8 Deposited 2012-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 78–328（251 aa） Fragment：unp residues 78-382	Mutation：A156C	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；1.5 M ammonium sulfate and 100 mM citrate, pH 5.5, EVAPORATION, temperature 293K	Resolution 2.52 Å R-free 0.267

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q63KH5_BURPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–281； UniProt 48–328 Author chain B； PDBConstruct 1–281； UniProt 48–328

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	3eir
Deposition date deposition_date	2008-09-17
Structure title title	Crystal structure of CHBP, a Cif Homologue from Burkholderia pseudomallei
Keywords keywords	papain-like fold, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	24.00 Å
Radius of gyration Rg (electron density) rg_electron	22.89 Å
Forward intensity I(0) i0	50868100.00
Molecular weight molecular_weight	54899.0 kDa
Excluded volume excluded_volume	68603 Å³
Envelope volume envelope_volume	82430 Å³
Hydration-shell volume shell_volume	29419 Å³
Envelope diameter envelope_diameter	80.8 Å
Shell Rg shell_rg	30.52 Å
Envelope Rg envelope_rg	22.81 Å
Shape Rg shape_rg	22.88 Å
Total Rg total_rg	23.78 Å
Total atoms total_atoms	3868
Residues n_residues	489
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	77.4 Å
Rg (real space) rg_real	23.84 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	5.0870e+07
I(0) uncertainty (real space) i0_real_error	7.1690e+05
Rg (reciprocal space) rg_reciprocal	23.88 Å
I(0) (reciprocal space) i0_reciprocal	50870000.0000
Solution quality estimate total_estimate	0.8139
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	0.157
Kurtosis Kurtosis kurtosis	-0.468
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13490000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	54.783 Å
Unit-cell length b length_b	79.916 Å
Unit-cell length c length_c	117.416 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.101 Å
Low-resolution limit resolution_low	33.033 Å
R factor r_factor	0.1990
R_work r_work	0.1930
R_free r_free	0.2540

Description description	Putative ATP/GTP binding protein
Molecular weight formula_weight	31308.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4121

Crystal structure of CHBP, a Cif Homologue from Burkholderia pseudomallei

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

Putative ATP/GTP binding 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Burkholderia pseudomallei
NCBI Class编号 ncbi_taxonomy_id	28450
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

fit	/app/data/saxs_computation/ei/3eir/3eir.fit
pddf	/app/data/pr_computation/ei/3eir/3eir.pr.out
profile	/app/data/saxs_computation/ei/3eir/3eir.dat