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2eyd

Water refined solution structure of crambin in dpc micelles

Method: SOLUTION NMR Dmax: 35.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CRAMBIN

Crambe hispanica subsp. abyssinica

UniProt P01542

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 1–46 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition：0.5 MM CRAMBIN U-15N,13C, PH 6.0, 20 MM PHOSPHATE BUFFER, 300MM DPC, 90% H2O, 10% D2O | 20 MM PHOSPHATE BUFFER, 300MM DPC, 90% H2O, 10% D2O Resolution not provided

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 2EYD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AB1 SI FORM CRAMBIN Deposited 1997-01-31 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions vapor diffusion - hanging drop - microseeding；pH 7；HPLC PURIFIED SI-CRAMBIN PROTEIN WAS DISSOLVED AT 25 MG/ML IN 80% ETHANOL/WATER (V/V), AND EQUILIBRATED AGAINS 60% ETHANOL. AFTER 10 DAYS, THE RESERVOIR WAS LOWERED TO 50% AND MICROSEEDED BY THE STREAK SEEDING METHOD (CAT WHISKER). AFTER LOWERING THE RESERVOIR TO 45%, GOOD CRYSTALS WERE FORMED., pH 7., vapor diffusion - hanging drop - microseeding
Resolution 0.89 Å
1CBN ATOMIC RESOLUTION (0.83 ANGSTROMS) CRYSTAL STRUCTURE OF THE HYDROPHOBIC PROTEIN CRAMBIN AT 130 K Deposited 1991-10-11 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 0.83 Å
1CCM DIRECT NOE REFINEMENT OF CRAMBIN FROM 2D NMR DATA USING A SLOW-COOLING ANNEALING PROTOCOL Deposited 1993-04-14 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1CCN DIRECT NOE REFINEMENT OF CRAMBIN FROM 2D NMR DATA USING A SLOW-COOLING ANNEALING PROTOCOL Deposited 1993-04-14 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1CNR CORRELATED DISORDER OF THE PURE PRO22(SLASH)LEU25 FORM OF CRAMBIN AT 150K REFINED TO 1.05 ANGSTROMS RESOLUTION Deposited 1993-07-15 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.05 Å
1CRN WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC RESOLUTION. PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF CRAMBIN Deposited 1981-04-30 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å
1CXR AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS Deposited 1999-08-30 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa） Fragment：ISOFORM OF CRAMBIN (46 RESIDUES)
Mutation：S22P, I25L No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure 1
NMR sample composition 2.5 MM CRAMBIN(SER/ILE) 0.7 ML OF 75% D6-ACETONE, 20%H2O,5%D2O BUFFER
Resolution not provided
1EJG CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY. Deposited 2000-03-02 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa） Fragment：CRAMBIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；The protein (40 mg/ml in 80% ethanol) is equilibrated against 60% ethanol. Not buffered., pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.54 Å R-free 0.094
1JXT CRAMBIN MIXED SEQUENCE FORM AT 160 K. PROTEIN/WATER SUBSTATES Deposited 2001-09-08 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；ethanol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.89 Å
1JXU CRAMBIN MIXED SEQUENCE FORM AT 240 K. PROTEIN/WATER SUBSTATES Deposited 2001-09-09 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；ethanol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.99 Å
1JXW CRAMBIN MIXED SEQUENCE FORM AT 180 K. PROTEIN/WATER SUBSTATES Deposited 2001-09-10 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；ethanol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.89 Å
1JXX CRAMBIN MIXED SEQUENCE FORM AT 200 K. PROTEIN/WATER SUBSTATES Deposited 2001-09-10 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；ethanol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.89 Å
1JXY CRAMBIN MIXED SEQUENCE FORM AT 220 K. PROTEIN/WATER SUBSTATES Deposited 2001-09-10 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；ethanol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.89 Å
1YV8 Solution structure of crambin in acetone/water mixed solvent Deposited 2005-02-15 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 1mM crambin U-15N,13C, 75% acetone, 15% H2O, 10% D2O | 75% acetone, 15% H2O, 10% D2O
Resolution not provided
1YVA NMR solution structure of crambin in DPC micelles Deposited 2005-02-15 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 0.5 mM crambin U-15N,13C, pH 6.0, 20 mM phosphate buffer, 300mM DPC, 90% H2O, 10% D2O | 300 mM DPC, 20 mM phosphate buffer, 90% H2O, 10% D2O
Resolution not provided
2EYA DMSO refined solution structure of crambin in acetone/water Deposited 2005-11-09 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 298 K；Pressure AMBIENT
NMR sample composition 1MM CRAMBIN U-15N,13C, 75% ACETONE, 15% H2O, 10% D2O | 75% ACETONE, 15% H2O, 10% D2O
Resolution not provided
2EYB Water refined solution structure of crambin in ACETONE/WATER Deposited 2005-11-09 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 1MM CRAMBIN U-15N,13C, 75% ACETONE, 15% H2O, 10% D2O | 75% ACETONE, 15% H2O, 10% D2O
Resolution not provided
2EYC DMSO refined solution structure of crambin in dpc micelles Deposited 2005-11-09 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 0.5 MM CRAMBIN U-15N,13C, PH 6.0, 20 MM PHOSPHATE BUFFER, 300MM DPC, 90% H2O, 10% D2O | 20 MM PHOSPHATE BUFFER, 300MM DPC, 90% H2O, 10% D2O
Resolution not provided
2FD7 X-ray Crystal Structure of Chemically Synthesized Crambin Deposited 2005-12-13 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；The native crambin crystals were grown from the aqueous solution by mixing a 2 ul aliquot of a crambin (10 mg/ml in pH 8.0, 100mM HEPES buffer containing 150mM NaCl) and 2 ul of a 0.8 M succinic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.75 Å R-free 0.185
2FD9 X-ray Crystal Structure of Chemically Synthesized Crambin-{alpha}carboxamide Deposited 2005-12-13 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；X-ray crystallography-quality crystals for crambin-carboxamide were formed by mixing 2 ul of protein (10 mg/ml in pH 7.5 100mM HEPES buffer containing 150 mM NaCl) and 2 ul of a 0.8 M succinic acid (used for X-ray diffraction), or by mixing 2 ul of the protein solution with 2 ul of 0.1 M HEPES buffer containing 15% v/v tacsimate and 2% w/v polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.60 Å R-free 0.234
3NIR Crystal structure of small protein crambin at 0.48 A resolution Deposited 2010-06-16 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；60% ethanol in water, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.48 Å
3U7T Room temperature ultra-high resolution time-of-flight neutron and X-ray diffraction studies of H/D exchanged crambin Deposited 2011-10-14 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Vapor diffusion of protein in 80 % EtOH solution against a 55 % EtOH solution, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 0.85 Å R-free 0.136
3UE7 X-ray crystal structure of a novel topological analogue of crambin Deposited 2011-10-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–46（46 aa） Fragment：L-crambin topological analogue
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；292 K；100 mM imidazole, 200 mM Zinc chloride, 7.5% Ethanol, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.08 Å R-free 0.176
3UE7 X-ray crystal structure of a novel topological analogue of crambin Deposited 2011-10-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–46（46 aa） Fragment：L-crambin topological analogue
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；292 K；100 mM imidazole, 200 mM Zinc chloride, 7.5% Ethanol, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.08 Å R-free 0.176
4FC1 Ultra-high resolution neutron structure of crambin at room-temperature Deposited 2012-05-23 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule NEUTRON DIFFRACTION
X-ray crystallization conditions 290 K；large crystals were obtained in 1mL crystallization drops containing 20-30mg/ml protein in 80% EtOH/H2O; the well solution was 60% EtOH/H2O; no mixing with well solution was done., VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 1.10 Å R-free 0.253
9EWK Solvent organization in ultrahigh-resolution protein crystal structure at room temperature Deposited 2024-04-04 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded EOH ETHANOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；80% (v/v) ethanol:water solution
Resolution 0.70 Å
9PIS Ab initio structure of crambin by MicroED at 0.85A Deposited 2025-07-11 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–46（46 aa）
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer pH 7；Simple mixture of ethanol and water.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 0.85 Å R-free 0.164

26 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRAM_CRAAB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–46； UniProt 1–46

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 2eyd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2eyd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2eyd
Deposition date deposition_date2005-11-09
Structure title titleWater refined solution structure of crambin in dpc micelles
Keywords keywordsCRAMBIN, DPC, MICELLES, PLANT PROTEIN; PLANT PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier9.19 Å
Radius of gyration Rg (electron density) rg_electron9.80 Å
Forward intensity I(0) i0141072000.00
Molecular weight molecular_weight94729.0 kDa
Excluded volume excluded_volume116380 ų
Envelope volume envelope_volume9506 ų
Hydration-shell volume shell_volume7782 ų
Envelope diameter envelope_diameter35.5 Å
Shell Rg shell_rg16.05 Å
Envelope Rg envelope_rg11.14 Å
Shape Rg shape_rg9.82 Å
Total Rg total_rg9.89 Å
Total atoms total_atoms12840
Residues n_residues920
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 dmax35.3 Å
Rg (real space) rg_real9.18 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real1.4110e+08
I(0) uncertainty (real space) i0_real_error1.7190e+06
Rg (reciprocal space) rg_reciprocal9.18 Å
I(0) (reciprocal space) i0_reciprocal141100000.0000
Solution quality estimate total_estimate0.8307
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary11.2 Å
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.412
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15160.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.685; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.754; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2eyda_
Class classg — Small proteins
Fold Fold foldg.13 — Crambin-like
Superfamily Superfamily superfamilyg.13.1 — Crambin-like
Family Family familyg.13.1.1 — Crambin-like

CATH v4.4 (1 domains)

Domain ID domain_id2eydA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1350 — Crambin
Homologous superfamily homologous superfamily10 — Thionin-like
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8. Citations (1)

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9. Files and Curves (10)