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- PDB-2fd7: X-ray Crystal Structure of Chemically Synthesized Crambin -

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Basic information

Entry
Database: PDB / ID: 2fd7
TitleX-ray Crystal Structure of Chemically Synthesized Crambin
ComponentsCrambin
KeywordsUNKNOWN FUNCTION / crambin
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBang, D. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.
CitationJournal: Mol Biosyst / Year: 2009
Title: Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide.
Authors: Bang, D. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 30, 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crambin


Theoretical massNumber of molelcules
Total (without water)4,7381
Polymers4,7381
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.924, 104.924, 104.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

21A-137-

HOH

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Components

#1: Protein/peptide Crambin


Mass: 4738.447 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The protein was chemically synthesized. The sequence of the protein can be naturally found in Crambe abyssinica (Abyssinian crambe).
References: UniProt: P01542
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The native crambin crystals were grown from the aqueous solution by mixing a 2 ul aliquot of a crambin (10 mg/ml in pH 8.0, 100mM HEPES buffer containing 150mM NaCl) and 2 ul of a 0.8 M ...Details: The native crambin crystals were grown from the aqueous solution by mixing a 2 ul aliquot of a crambin (10 mg/ml in pH 8.0, 100mM HEPES buffer containing 150mM NaCl) and 2 ul of a 0.8 M succinic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.75→30 Å / Num. all: 9519 / Num. obs: 9070
Reflection shellResolution: 1.75→1.795 Å

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Processing

SoftwareName: REFMAC / Version: 5.1.9999 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.188 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18476 449 4.7 %RANDOM
Rwork0.15887 ---
all0.16014 ---
obs0.16014 9070 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.323 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms325 0 0 80 405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022336
X-RAY DIFFRACTIONr_bond_other_d0.0050.02295
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.97464
X-RAY DIFFRACTIONr_angle_other_deg2.2563691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.982545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2682310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3811543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.067152
X-RAY DIFFRACTIONr_chiral_restr0.0630.255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0261
X-RAY DIFFRACTIONr_nbd_refined0.2210.268
X-RAY DIFFRACTIONr_nbd_other0.1930.2296
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0140.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1340.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9771.5296
X-RAY DIFFRACTIONr_mcbond_other0.2051.593
X-RAY DIFFRACTIONr_mcangle_it1.1052376
X-RAY DIFFRACTIONr_scbond_it1.9333125
X-RAY DIFFRACTIONr_scangle_it2.8314.588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.455 15
Rwork0.346 334
Refinement TLS params.Method: refined / Origin x: -0.5131 Å / Origin y: 37.3508 Å / Origin z: 57.6295 Å
111213212223313233
T-0.0359 Å2-0.0022 Å2-0.0048 Å2--0.0334 Å2-0.0007 Å2---0.0338 Å2
L2.75 °21.542 °2-1.0611 °2-1.3766 °2-0.7058 °2--2.0825 °2
S-0.1056 Å °0.1859 Å °-0.0482 Å °-0.1035 Å °0.0866 Å °0.0286 Å °0.1276 Å °-0.1297 Å °0.0189 Å °

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