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- PDB-1ejg: CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY. -

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Basic information

Entry
Database: PDB / ID: 1ejg
TitleCRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY.
ComponentsCRAMBIN (PRO22,SER22/LEU25,ILE25)
KeywordsPLANT PROTEIN / VALENCE ELECTRON DENSITY / MULTI-SUBSTATE / MULTIPOLE REFINEMENT
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 / SYNCHROTRON / Resolution: 0.54 Å
AuthorsJelsch, C. / Teeter, M.M. / Lamzin, V. / Pichon-Lesme, V. / Blessing, B. / Lecomte, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
Authors: Jelsch, C. / Teeter, M.M. / Lamzin, V. / Pichon-Pesme, V. / Blessing, R.H. / Lecomte, C.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: 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: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
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 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRAMBIN (PRO22,SER22/LEU25,ILE25)


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)40.824, 18.498, 22.371
Angle α, β, γ (deg.)90.00, 90.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide CRAMBIN (PRO22,SER22/LEU25,ILE25)


Mass: 4738.447 Da / Num. of mol.: 1 / Fragment: CRAMBIN / Source method: isolated from a natural source
Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542
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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein (40 mg/ml in 80% ethanol) is equilibrated against 60% ethanol. Not buffered., pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Teeter, M.M., (1993) J. Mol. Biol., 230, 292.
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 31, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.54 Å / Relative weight: 1
ReflectionResolution: 0.54→50 Å / Num. obs: 79868 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 2.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 8.2
Reflection shellResolution: 0.54→0.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.1476 / % possible all: 100
Reflection
*PLUS
Highest resolution: 0.54 Å / Lowest resolution: 50 Å / Num. all: 112293 / Num. obs: 79869 / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Num. measured all: 489969
Reflection shell
*PLUS
Redundancy: 3.8 %

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Processing

Software
NameClassification
DREARdata reduction
MOLLYrefinement
DREARdata scaling
RefinementResolution: 0.54→22.37 Å / σ(F): 0
Details: SHELX97 FOLLOWED BY MOLLY (N.K.HANSEN & P.COPPENS ACTA CRYSTALLOGR. A34, 909-921) REFINEMENT OF ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.094 11220 5 %1 REFLECTION OUT OF 20
Rwork0.09 ---
obs-100989 97.6 %-
Refinement stepCycle: LAST / Resolution: 0.54→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms340 0 0 0 340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.023
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.7
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 0.54→0.57 Å
RfactorNum. reflection% reflection
Rfree0.205 -5 %
Rwork0.197 17547 -
Xplor fileSerial no: 1 / Param file: SHELXL97 DICTIONARY
Software
*PLUS
Name: MOLLY / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.09 / Rfactor Rwork: 0.09
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.205 / % reflection Rfree: 5 % / Rfactor Rwork: 0.197

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