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- PDB-3sbn: trichovirin I-4A in polar environment at 0.9 Angstroem -

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Basic information

Entry
Database: PDB / ID: 3sbn
Titletrichovirin I-4A in polar environment at 0.9 Angstroem
ComponentsTrichovirin I-4A
KeywordsANTIBIOTIC / curved 310-helix / 3-10 HELIX / peptide antibiotic
Function / homologyTrichovirin I-4A / ACETONITRILE / METHANOL / :
Function and homology information
Biological speciesHypocrea rufa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.9 Å
AuthorsGessmann, R. / Axford, D. / Petratos, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Four complete turns of a curved 310-helix at atomic resolution: The crystal structure of the peptaibol trichovirin I-4A in polar environment suggests a transition to alpha-helix for membrane function
Authors: Gessmann, R. / Axford, D. / Owen, R.L. / Bruckner, H. / Petratos, K.
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trichovirin I-4A
B: Trichovirin I-4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8886
Polymers2,7412
Non-polymers1464
Water28816
1
A: Trichovirin I-4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4533
Polymers1,3711
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trichovirin I-4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4353
Polymers1,3711
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.284, 9.896, 37.567
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthor states that the biologically significant oligomerization state in apolar environment is not represented in the monomeric structure. The stoichiometry of the oligomer in the membrane is unknown.

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Components

#1: Protein/peptide Trichovirin I-4A


Type: Peptaibol / Class: Antibiotic / Mass: 1370.722 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Equivalent to Harzianin HC-VI from Trichoderma harzianum
Source: (natural) Hypocrea rufa (fungus) / Strain: NRRL 5243 / References: NOR: NOR00990, Trichovirin I-4A
#2: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR CONFIRMS THAT THERE ARE TWO IDENTICAL ANITBOTICS UNDER DIFFERENT NAMES FROM DIFFERENT SOUCES ...AUTHOR CONFIRMS THAT THERE ARE TWO IDENTICAL ANITBOTICS UNDER DIFFERENT NAMES FROM DIFFERENT SOUCES AS SEEN BETWEEN THE NORINE ENTRY NOR00990 USED FOR THE SEQUENCE REFERENCE AND THIS ENTRY.

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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: 1.61 Å3/Da / Density % sol: 23.8 %
Crystal growTemperature: 293 K / pH: 7
Details: methanol, acetonitrile, water, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.7469
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2009
Details: OXFORD DANFYSIK/SESO TWO STAGE DEMAGNIFICATION USING TWO K-B PAIRS OF BIMORPH T YPE MIRRORS
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7469 Å / Relative weight: 1
ReflectionResolution: 0.9→37.3 Å / Num. obs: 13524 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 6.15 Å2 / Net I/σ(I): 13.2
Reflection shellResolution: 0.9→0.95 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.1 / % possible all: 91.6

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Processing

Software
NameClassification
GDAdata collection
ACORNphasing
SHELXLrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.9→37.3 Å / Num. parameters: 2134 / Num. restraintsaints: 2263 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.128 679 5 %RANDOM
obs0.102 -98.4 %-
all-13524 --
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 230 / Occupancy sum non hydrogen: 212.5
Refinement stepCycle: LAST / Resolution: 0.9→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms196 0 10 16 222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.045
X-RAY DIFFRACTIONs_angle_d0.076
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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