9z6r

Crystal Structure of CBS domain containing protein from Burkholderia phymatum

Method: X-RAY DIFFRACTION Dmax: 69.0 Å Quality: REASONABLE

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

CBS domain containing protein

Paraburkholderia phymatum STM815

UniProt B2JRV0

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 1–120 Chain B; UniProt 1–120 Fragment:1-120 ACT ACETATE ION × 1 CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;291 K;Berkeley A2: 100 mM sodium acetate, pH 4.5, 2 M sodium formate. BuphA.00062.a.B2.PW39454 at 37 mg/mL. plate 20515 A2 drop 2, Puck: PSL-0210, Cryo: 80% crystallant + 20% PEG 200 Resolution 1.39 Å R-free 0.194

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name B2JRV0_PARP8
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 9–128; UniProt 1–120 Author chain B; PDBConstruct 9–128; UniProt 1–120

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9z6r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9z6r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9z6r
Deposition date deposition_date2025-11-14
最后修订 last_revision2025-11-26
Structure title titleCrystal Structure of CBS domain containing protein from Burkholderia phymatum
Keywords keywords;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, CBS domain containing protein, Burkholderia phymatum, UNKNOWN FUNCTION ;; UNKNOWN FUNCTION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.06
Radius of gyration Rg (electron density) rg_electron20.18
Forward intensity I(0) i013171000.00
Molecular weight molecular_weight25992.0 kDa
Excluded volume excluded_volume32131 ų
Envelope volume envelope_volume39778 ų
Hydration-shell volume shell_volume17194 ų
Envelope diameter envelope_diameter69.7
Shell Rg shell_rg25.64
Envelope Rg envelope_rg20.30
Shape Rg shape_rg20.22
Total Rg total_rg20.86
Total atoms total_atoms1808
Residues n_residues237
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.0
Rg (real space) rg_real21.08
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real1.3170e+07
I(0) uncertainty (real space) i0_real_error1.6600e+05
Rg (reciprocal space) rg_reciprocal21.08
I(0) (reciprocal space) i0_reciprocal13170000.0000
Solution quality estimate total_estimate0.7158
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.3
Skewness Skewness skewness0.335
Kurtosis Kurtosis kurtosis-0.459
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4264000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 0.225; Positv: 1.000; Valcen: 0.952; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)