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- PDB-1crn: WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC RESOLUTION. PE... -

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Basic information

Entry
Database: PDB / ID: 1crn
TitleWATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC RESOLUTION. PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF CRAMBIN
ComponentsCRAMBIN
KeywordsPLANT PROTEIN / PLANT SEED PROTEIN
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 / Resolution: 1.5 Å
AuthorsHendrickson, W.A. / Teeter, M.M.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 1984
Title: Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin.
Authors: Teeter, M.M.
#1: Journal: Nature / Year: 1981
Title: Structure of the Hydrophobic Protein Crambin Determined Directly from the Anomalous Scattering of Sulphur
Authors: Hendrickson, W.A. / Teeter, M.M.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: Highly Ordered Crystals of the Plant Seed Protein Crambin
Authors: Teeter, M.M. / Hendrickson, W.A.
History
DepositionApr 30, 1981Processing site: BNL
Revision 1.0Jul 28, 1981Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 11, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRAMBIN


Theoretical massNumber of molelcules
Total (without water)4,7381
Polymers4,7381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.960, 18.650, 22.520
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide CRAMBIN


Mass: 4738.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542
Compound detailsTHE SECONDARY STRUCTURE SPECIFICATIONS ARE THOSE DEFINED IN REFERENCE 1 ABOVE AND DEPEND ON ...THE SECONDARY STRUCTURE SPECIFICATIONS ARE THOSE DEFINED IN REFERENCE 1 ABOVE AND DEPEND ON PARTICULAR DEFINITIONS THAT MAY AFFECT THE DETERMINATION OF END POINTS. PLEASE CONSULT THE PRIMARY REFERENCE AND EXAMINE STRUCTURAL DETAILS SUCH AS HYDROGEN BONDING AND CONFORMATION ANGLES WHEN MAKING USE OF THE SPECIFICATIONS.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.16 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 60 % / Common name: ethanol

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 21045 / Observed criterion σ(F): 2 / Rmerge F obs: 0.129

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms327 0 0 0 327
Refinement
*PLUS
Num. reflection obs: 6300 / Rfactor obs: 0.144
Solvent computation
*PLUS
Displacement parameters
*PLUS

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