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- PDB-1cbn: ATOMIC RESOLUTION (0.83 ANGSTROMS) CRYSTAL STRUCTURE OF THE HYDRO... -

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Basic information

Entry
Database: PDB / ID: 1cbn
TitleATOMIC RESOLUTION (0.83 ANGSTROMS) CRYSTAL STRUCTURE OF THE HYDROPHOBIC PROTEIN CRAMBIN AT 130 K
ComponentsCRAMBIN
KeywordsPLANT 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: 0.83 Å
AuthorsTeeter, M.M. / Roe, S.M. / Heo, N.H.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Atomic resolution (0.83 A) crystal structure of the hydrophobic protein crambin at 130 K.
Authors: Teeter, M.M. / Roe, S.M. / Heo, N.H.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Cryocrystallography of Biological Macromolecules: A Generally Applicable Method
Authors: Hope, H.
#2: Journal: J.Am.Chem.Soc. / Year: 1986
Title: An Empirical Examination of Potential Energy Minimization Using the Well-Determined Structure of the Protein Crambin
Authors: Whitlow, M. / Teeter, M.M.
#3: Journal: Ann.N.Y.Acad.Sci. / Year: 1986
Title: Progress in the Water Structure of the Protein Crambin by X-Ray Diffraction at 140 K
Authors: Teeter, M.M. / Hope, H.
#4: 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.
#5: 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.
#6: Journal: J.Mol.Biol. / Year: 1979
Title: Highly Ordered Crystals of the Plant Seed Protein Crambin
Authors: Teeter, M.M. / Hendrickson, W.A.
History
DepositionOct 11, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Feb 5, 2014Group: Atomic model / 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 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET IN SHEET *S1*, STRAND 3 IS QUESTIONABLY A STRAND. IN SHEET *S2*, STRAND 1 HAS NO HYDROGEN ...SHEET IN SHEET *S1*, STRAND 3 IS QUESTIONABLY A STRAND. IN SHEET *S2*, STRAND 1 HAS NO HYDROGEN BONDS. THE BACKBONE ATOMS ARE IN BETA CONFORMATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRAMBIN
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)40.763, 18.492, 22.333
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide CRAMBIN


Mass: 4728.410 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
#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

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.9 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
280 %(v/v)ethanol1drop
360 %ethanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 0.826 Å / Lowest resolution: 10 Å / Num. all: 33221 / Num. obs: 26969 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.123
Reflection shell
*PLUS
Highest resolution: 0.83 Å / Lowest resolution: 0.85 Å / % possible obs: 91.5 % / Rmerge(I) obs: 0.215

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.106 / Highest resolution: 0.83 Å
Refinement stepCycle: LAST / Highest resolution: 0.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms341 0 3 0 344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.83 Å / Lowest resolution: 10 Å / Rfactor obs: 0.106
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.0410.041
X-RAY DIFFRACTIONp_planar_d0.050.057
X-RAY DIFFRACTIONp_chiral_restr0.050.078

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