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- PDB-2fd9: X-ray Crystal Structure of Chemically Synthesized Crambin-{alpha}... -

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Basic information

Entry
Database: PDB / ID: 2fd9
TitleX-ray Crystal Structure of Chemically Synthesized Crambin-{alpha}carboxamide
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: 1.6 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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crambin


Theoretical massNumber of molelcules
Total (without water)4,7381
Polymers4,7381
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.581, 67.581, 39.487
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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.: 10 / 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

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: X-ray crystallography-quality crystals for crambin-carboxamide were formed by mixing 2 ul of protein (10 mg/ml in pH 7.5 100mM HEPES buffer containing 150 mM NaCl) and 2 ul of a 0.8 M ...Details: X-ray crystallography-quality crystals for crambin-carboxamide were formed by mixing 2 ul of protein (10 mg/ml in pH 7.5 100mM HEPES buffer containing 150 mM NaCl) and 2 ul of a 0.8 M succinic acid (used for X-ray diffraction), or by mixing 2 ul of the protein solution with 2 ul of 0.1 M HEPES buffer containing 15% v/v tacsimate and 2% w/v polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 4566 / Num. obs: 4354
Reflection shellResolution: 1.601→1.643 Å

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Processing

SoftwareName: REFMAC / Version: 5.1.9999 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.472 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23385 212 4.6 %RANDOM
Rwork0.21552 ---
all0.2165 4566 --
obs0.2165 4354 97.73 %-
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: 31.739 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å21.3 Å20 Å2
2--2.59 Å20 Å2
3----3.89 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms299 0 0 10 309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022308
X-RAY DIFFRACTIONr_bond_other_d0.0040.02278
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.972425
X-RAY DIFFRACTIONr_angle_other_deg0.9643650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.117542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.98522.58
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8621540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.58152
X-RAY DIFFRACTIONr_chiral_restr0.0720.252
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0254
X-RAY DIFFRACTIONr_nbd_refined0.2270.266
X-RAY DIFFRACTIONr_nbd_other0.1980.2253
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.22
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1550.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1011.5278
X-RAY DIFFRACTIONr_mcbond_other0.2161.587
X-RAY DIFFRACTIONr_mcangle_it1.422350
X-RAY DIFFRACTIONr_scbond_it2.3063107
X-RAY DIFFRACTIONr_scangle_it2.9224.575
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 12
Rwork0.295 279
Refinement TLS params.Method: refined / Origin x: 0.9386 Å / Origin y: 17.8807 Å / Origin z: 4.9781 Å
111213212223313233
T-0.1298 Å2-0.0658 Å20.003 Å2-0.2326 Å2-0.016 Å2--0.0363 Å2
L2.9916 °2-0.0796 °20.4556 °2-5.4938 °20.1429 °2--11.8568 °2
S-0.0844 Å °0.1432 Å °-0.0178 Å °-0.0903 Å °-0.0173 Å °0.5092 Å °0.2321 Å °-1.8853 Å °0.1017 Å °

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