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4w9a

Crystal structure of Gamma-B Crystallin expressed in E. coli based on mRNA variant 2

Method: X-RAY DIFFRACTION Dmax: 56.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Gamma-crystallin B

Bos taurus

UniProt P02526

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 1–175 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1% Trypton, 20% PEG 3350, 50mM HEPES Resolution 1.38 Å R-free 0.184

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 4W9A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AMM 1.2 ANGSTROM STRUCTURE OF GAMMA-B CRYSTALLIN AT 150K Deposited 1996-03-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–174（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.20 Å
1DSL GAMMA B CRYSTALLIN C-TERMINAL DOMAIN Deposited 1996-02-01 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 87–174（88 aa） Fragment：C-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.55 Å
1GAM GAMMA B CRYSTALLIN TRUNCATED C-TERMINAL DOMAIN Deposited 1996-02-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 87–172（86 aa） Fragment：TRUNCATED C-TERMINAL DOMAIN
Chain B 87–172（86 aa） Fragment：TRUNCATED C-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1GCS STRUCTURE OF THE BOVINE GAMMA-B CRYSTALLIN AT 150K Deposited 1994-01-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–174（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1I5I THE C18S MUTANT OF BOVINE (GAMMA-B)-CRYSTALLIN Deposited 2001-02-27 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–174（174 aa）
Mutation：C18S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions chill tube containing protein to 265 K, then bring to 295 K；pH 7；295 K；100 mM Phosphate, 20 mM DTT, pH 7.0, chill tube containing protein to 265 K, then bring to 295 K
Resolution 2.40 Å R-free 0.243
4GCR STRUCTURE OF THE BOVINE EYE LENS PROTEIN GAMMA-B (GAMMA-II)-CRYSTALLIN AT 1.47 ANGSTROMS Deposited 1992-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–174（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.47 Å
4W9B Crystal structure of Gamma-B Crystallin expressed in E. coli based on mRNA variant 1 Deposited 2014-08-27 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 1–175（175 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1% Trypton, 20% PEG 3350, 50mM HEPES
Resolution 1.28 Å R-free 0.188
6QDW Cryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptide Deposited 2019-01-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 32-meric
Chain z 1–38（38 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Tico Buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
6YS3 Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled GBC SecM peptide Deposited 2020-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 32-meric
Chain z 1–38（38 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRGB_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–175； UniProt 1–175

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 4w9a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4w9a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4w9a
Deposition date deposition_date2014-08-27
Structure title titleCrystal structure of Gamma-B Crystallin expressed in E. coli based on mRNA variant 2
Keywords keywordsEye lens protein, structural protein; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.67 Å
Radius of gyration Rg (electron density) rg_electron16.52 Å
Forward intensity I(0) i08720180.00
Molecular weight molecular_weight20638.0 kDa
Excluded volume excluded_volume25243 ų
Envelope volume envelope_volume28235 ų
Hydration-shell volume shell_volume14722 ų
Envelope diameter envelope_diameter58.8 Å
Shell Rg shell_rg21.92 Å
Envelope Rg envelope_rg16.75 Å
Shape Rg shape_rg16.51 Å
Total Rg total_rg17.40 Å
Total atoms total_atoms1450
Residues n_residues172
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax56.9 Å
Rg (real space) rg_real17.65 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real8.7200e+06
I(0) uncertainty (real space) i0_real_error1.1650e+05
Rg (reciprocal space) rg_reciprocal17.65 Å
I(0) (reciprocal space) i0_reciprocal8720000.0000
Solution quality estimate total_estimate0.8115
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.5 Å
Skewness Skewness skewness0.336
Kurtosis Kurtosis kurtosis-0.324
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1847000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; 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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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4w9aa_
Class classb — All beta proteins
Fold Fold foldb.11 — gamma-Crystallin-like
Superfamily Superfamily superfamilyb.11.1 — gamma-Crystallin-like
Family Family familyb.11.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id4w9aA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology20 — Gamma-B Crystallin; domain 1
Homologous superfamily homologous superfamily10 — Crystallins
Domain ID domain_id4w9aA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology20 — Gamma-B Crystallin; domain 1
Homologous superfamily homologous superfamily10 — Crystallins
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8. Citations (1)

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9. Files and Curves (10)