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- PDB-1jxu: CRAMBIN MIXED SEQUENCE FORM AT 240 K. PROTEIN/WATER SUBSTATES -

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Basic information

Entry
Database: PDB / ID: 1jxu
TitleCRAMBIN MIXED SEQUENCE FORM AT 240 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: 0.99 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 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Aug 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
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)40.900, 18.590, 22.400
Angle α, β, γ (deg.)90.00, 90.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly not known.

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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
Sequence detailssequence PRO/SER22:LEU/ILE25 SEQUENCE ISOFORMS ARE MODELLED AS ALTERNATE CONFORMERS IN COORDINATE ...sequence PRO/SER22:LEU/ILE25 SEQUENCE ISOFORMS ARE MODELLED AS ALTERNATE CONFORMERS IN COORDINATE RECORDS. ONLY THE PRO22/LEU25 ISOFORM IS REPRESENTED IN THE SEQUENCE RECORDS.

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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: 240 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Dec 25, 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: 0.99→17.67 Å / Num. all: 7272 / Num. obs: 7272 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1 % / Net I/σ(I): 17.2
Reflection shellResolution: 0.99→1 Å / Redundancy: 1 % / Mean I/σ(I) obs: 4.4 / % possible all: 0.162
Reflection
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.139

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Processing

Software
NameClassification
LEHMANN-LARSENdata collection
TEXSANdata reduction
PROLSQrefinement
LEHMANN-LARSENdata reduction
TEXSANdata scaling
RefinementStarting model: 1JXY. CRAMBIN MIXED ISOFORM AT 220 K.

1jxy


Resolution: 0.99→17.67 Å / Cross valid method: DIFFERENCE DENSITY PEAKS / σ(F): 2 / σ(I): 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).
RfactorNum. reflection% reflection
Rwork0.09 --
all0.09 --
obs0.09 7043 91.9 %
Displacement parametersBiso mean: 5.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.06 Å / Luzzati d res low obs: 17.67 Å
Refinement stepCycle: LAST / Resolution: 0.99→17.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms341 0 3 0 344
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.0060.01
X-RAY DIFFRACTIONp_mcbond_it0.1581
X-RAY DIFFRACTIONp_mcangle_it0.1751.5
X-RAY DIFFRACTIONp_scbond_it0.1761
X-RAY DIFFRACTIONp_scangle_it0.1161.5
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.0570.05
X-RAY DIFFRACTIONp_singtor_nbd0.1460.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.0720.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.1290.5
X-RAY DIFFRACTIONp_planar_tor53
X-RAY DIFFRACTIONp_staggered_tor1015
X-RAY DIFFRACTIONp_transverse_tor1620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.09 / Rfactor Rwork: 0.09
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 5.5 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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