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- PDB-1jxw: CRAMBIN MIXED SEQUENCE FORM AT 180 K. PROTEIN/WATER SUBSTATES -

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Basic information

Entry
Database: PDB / ID: 1jxw
TitleCRAMBIN MIXED SEQUENCE FORM AT 180 K. PROTEIN/WATER SUBSTATES
ComponentsCrambin
KeywordsPLANT PROTEIN / WATER / SUBSTATE / FUNCTION
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: 0.89 Å
AuthorsTeeter, M.M. / Yamano, A. / Stec, B. / Mohanty, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: On the nature of a glassy state of matter in a hydrated protein: Relation to protein function.
Authors: Teeter, M.M. / Yamano, A. / Stec, B. / Mohanty, U.
History
DepositionSep 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Feb 5, 2014Group: Atomic model / Other
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Oct 30, 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
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)40.860, 18.520, 22.390
Angle α, β, γ (deg.)90.00, 90.68, 90.00
Int Tables number4
Space group name H-MP1211
DetailsNot known but may be monomer

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Components

#1: Protein/peptide Crambin


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: 1.4 Å3/Da / Density % sol: 30 %
Description: VALUES OF F/SIGF ARE GIVEN ABOVE RATHER THAN I/SIGI.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ethanol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Dec 12, 1990 / Details: COLLIMATOR
RadiationMonochromator: MO / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.89→17.67 Å / Num. all: 26469 / Num. obs: 26469 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1 % / Biso Wilson estimate: 3.68 Å2 / Net I/σ(I): 10.6
Reflection shellResolution: 0.89→0.91 Å / Mean I/σ(I) obs: 2.7 / % possible all: 59
Reflection
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
LEHMANN-LARSENdata collection
TEXSANdata reduction
PROLSQrefinement
LEHMANN-LARSENdata reduction
TEXSANdata scaling
RefinementStarting model: 1JXT. CRAMBIN MIXED FORM AT 160 K.

1jxt


Resolution: 0.89→17.67 Å / Cross valid method: DIFFERENCE DENSITY PEAKS / σ(F): 2
Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667). WITH PROLSQ, NO RFREE WAS CALCULATED. ********* STEREOCHEMISTRY REMARKS: BECAUSE discretely disordered (MULTIPLE SUBSTATE) ...Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667). WITH PROLSQ, NO RFREE WAS CALCULATED. ********* STEREOCHEMISTRY REMARKS: BECAUSE discretely disordered (MULTIPLE SUBSTATE) PROTEIN RESIDUES EACH HAVE OCCUPANCY LESS THAN ONE, THEY ARE DIFFICULT TO ACCURATELY REFINE. THE GEOMETRY CAN BE DISTORTED (IS POORLY DETERMINED). IN THE CASE OF THR39, THE BACKBONE IS CLEARLY DISORDERED, WITH VERY SMALL DEVIATIONS BETWEEN SUBSTATES (~0.1 A), AND THAT WAS NOT INCLUDED IN THE MODEL. HENCE THEre may be LARGE ERRORS INVOLVING CA.
RfactorNum. reflection% reflection
Rwork0.137 --
obs0.137 23365 89 %
Displacement parametersBiso mean: 4 Å2
Refine analyzeLuzzati coordinate error obs: 0.06 Å / Luzzati d res low obs: 17.67 Å
Refinement stepCycle: LAST / Resolution: 0.89→17.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms341 0 3 0 344
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0060.01
X-RAY DIFFRACTIONp_mcbond_it0.1151
X-RAY DIFFRACTIONp_mcangle_it0.1171.5
X-RAY DIFFRACTIONp_scbond_it0.1441
X-RAY DIFFRACTIONp_scangle_it0.1521.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.0570.05
X-RAY DIFFRACTIONp_singtor_nbd0.1490.5
X-RAY DIFFRACTIONp_multtor_nbd0.1650.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.040.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.050.5
X-RAY DIFFRACTIONp_planar_tor53
X-RAY DIFFRACTIONp_staggered_tor9.415
X-RAY DIFFRACTIONp_transverse_tor12.820
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_mcbond_it1
X-RAY DIFFRACTIONp_scbond_it1
X-RAY DIFFRACTIONp_mcangle_it1.5
X-RAY DIFFRACTIONp_scangle_it1.5

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