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- PDB-1ab1: SI FORM CRAMBIN -

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Basic information

Entry
Database: PDB / ID: 1ab1
TitleSI FORM CRAMBIN
ComponentsCRAMBIN (SER22/ILE25)
KeywordsPLANT SEED PROTEIN / THIONIN
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodX-RAY DIFFRACTION / ALREADY SOLVED / Resolution: 0.89 Å
AuthorsTeeter, M.M. / Yamano, A.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Crystal structure of Ser-22/Ile-25 form crambin confirms solvent, side chain substate correlations.
Authors: Yamano, A. / Heo, N.H. / Teeter, M.M.
History
DepositionJan 31, 1997Processing site: BNL
Revision 1.0Aug 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 19, 2016Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRAMBIN (SER22/ILE25)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7742
Polymers4,7281
Non-polymers461
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.759, 18.404, 22.273
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide CRAMBIN (SER22/ILE25)


Mass: 4728.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.37 %
Crystal growMethod: vapor diffusion - hanging drop - microseeding / pH: 7
Details: 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 ...Details: 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
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: Teeter, M.M., (1979) J. Mol. Biol., 127, 219.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein solution1drop
280 %(v/v)ethanol1drop
350 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1992 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.89→17.67 Å / Num. obs: 23165 / % possible obs: 88.77 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Rmerge(I) obs: 0.04 / Rsym value: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 0.89→0.897 Å / Redundancy: 0.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.15 / % possible all: 74.96

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Processing

Software
NameClassification
LEHMANN-LARSENdata collection
TEXSANdata reduction
PROLSQrefinement
LEHMANN-LARSENdata reduction
TEXSANdata scaling
RefinementMethod to determine structure: ALREADY SOLVED / Resolution: 0.89→10 Å / Cross valid method: DIFFERENCE DENSITY PEAKS / σ(F): 2
Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667) THIS STRUCTURE ILLUSTRATES THE CONFIRMATION OF THE ABILITY OF X-RAY DIFFRACTION TO DETECT SUBSTATES. HERE THE SUBSTATES WERE ...Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667) THIS STRUCTURE ILLUSTRATES THE CONFIRMATION OF THE ABILITY OF X-RAY DIFFRACTION TO DETECT SUBSTATES. HERE THE SUBSTATES WERE PHYSICALLY SEPARATED (TWO SEQUENCE FORMS OF CRAMBIN) AND SEPARATE STRUCTURES DETERMINED. FURTHER SUBSTATES ARE EXTENDED FROM PROTEIN TO SURROUNDING SOLVENT.
RfactorNum. reflection% reflection
obs0.147 19803 84.6 %
Displacement parametersBiso mean: 5.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.08 Å / Luzzati d res low obs: 17.6 Å
Refinement stepCycle: LAST / Resolution: 0.89→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms326 0 3 0 329
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.010.006
X-RAY DIFFRACTIONp_mcbond_it0.111
X-RAY DIFFRACTIONp_mcangle_it0.111.5
X-RAY DIFFRACTIONp_scbond_it0.1361
X-RAY DIFFRACTIONp_scangle_it0.1361.5
X-RAY DIFFRACTIONp_plane_restr0.010.01
X-RAY DIFFRACTIONp_chiral_restr0.0630.05
X-RAY DIFFRACTIONp_singtor_nbd0.1580.5
X-RAY DIFFRACTIONp_multtor_nbd0.160.5
X-RAY DIFFRACTIONp_xhyhbond_nbd00.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.1580.5
X-RAY DIFFRACTIONp_planar_tor5.13
X-RAY DIFFRACTIONp_staggered_tor10.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.620
X-RAY DIFFRACTIONp_special_tor015

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