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- PDB-1cnr: CORRELATED DISORDER OF THE PURE PRO22(SLASH)LEU25 FORM OF CRAMBIN... -

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Basic information

Entry
Database: PDB / ID: 1cnr
TitleCORRELATED DISORDER OF THE PURE PRO22(SLASH)LEU25 FORM OF CRAMBIN AT 150K REFINED TO 1.05 ANGSTROMS RESOLUTION
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: 1.05 Å
AuthorsYamano, A. / Teeter, M.M.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Correlated disorder of the pure Pro22/Leu25 form of crambin at 150 K refined to 1.05-A resolution.
Authors: Yamano, A. / Teeter, M.M.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Atomic Resolution (0.83 Angstroms) Crystal Structure of the Hydrophobic Protein Crambin at 130K
Authors: Teeter, M.M. / Roe, S.M. / Heo, N.H.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Cryocrystallography of Biological Macromolecules: A Generally Applicable Method
Authors: Hope, H.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1979
Title: Highly Ordered Crystals of the Plant Seed Protein Crambin
Authors: Teeter, M.M. / Hendrickson, W.A.
History
DepositionJul 15, 1993Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Nov 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET S2 CONSISTS OF ONE STRAND WITH NO HYDROGEN BONDS. ONLY THE BACKBONE ATOMS ARE BETA.

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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)4,7852
Polymers4,7381
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)40.621, 18.345, 22.140
Angle α, β, γ (deg.)90.00, 91.03, 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
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: CRAM_CRAAB SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ILE 25 LEU 25 SEE REMARK 3.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.34 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein solution1drop
280 %(v/v)ethanol1drop
360 %ethanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.05 Å / Num. obs: 14765 / % possible obs: 93.85 %
Reflection shell
*PLUS
Highest resolution: 1.05 Å / Lowest resolution: 1.07 Å / Num. unique obs: 363

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.105 / Highest resolution: 1.05 Å
Refinement stepCycle: LAST / Highest resolution: 1.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms327 0 3 0 330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0410.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.05
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_restr0.0270.02
X-RAY DIFFRACTIONp_chiral_restr0.0780.05
X-RAY DIFFRACTIONp_singtor_nbd0.0720.01
X-RAY DIFFRACTIONp_multtor_nbd0.0440.01
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1490.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.93
X-RAY DIFFRACTIONp_staggered_tor9.315
X-RAY DIFFRACTIONp_orthonormal_tor12.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.105
Solvent computation
*PLUS
Displacement parameters
*PLUS

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