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- PDB-4z0w: Peptaibol gichigamin isolated from Tolypocladium sup_5 -

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Basic information

Entry
Database: PDB / ID: 4z0w
TitlePeptaibol gichigamin isolated from Tolypocladium sup_5
ComponentsPEPTAIBOL GICHIGAMIN
KeywordsANTIBIOTIC / PEPTAIBOL / ANTI-CANCER / TAIBOL
Biological speciesTolypocladium sp. Sup5 PDA-1 (fungus)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.1 Å
AuthorsDu, L. / Risinger, A.L. / Mitchell, C.A. / Stamps, B.W. / Pan, N. / King, J.B. / Motley, J.L. / Thomas, L.M. / Yang, Z. / Stevenson, B.S. ...Du, L. / Risinger, A.L. / Mitchell, C.A. / Stamps, B.W. / Pan, N. / King, J.B. / Motley, J.L. / Thomas, L.M. / Yang, Z. / Stevenson, B.S. / Mooberry, S.L. / Cichewicz, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM107490-01A1 United States
CitationJournal: TO BE PUBLISHED
Title: Peptaibol gichigamin isolated from Tolypocladium sup_5
Authors: Du, L. / Risinger, A.L. / Mitchell, C.A. / Stamps, B.W. / Pan, N. / King, J.B. / Motley, J.L. / Thomas, L.M. / Yang, Z. / Stevenson, B.S. / Mooberry, S.L. / Cichewicz, R.H.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTAIBOL GICHIGAMIN
B: PEPTAIBOL GICHIGAMIN


Theoretical massNumber of molelcules
Total (without water)4,0292
Polymers4,0292
Non-polymers00
Water1629
1
A: PEPTAIBOL GICHIGAMIN


Theoretical massNumber of molelcules
Total (without water)2,0141
Polymers2,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PEPTAIBOL GICHIGAMIN


Theoretical massNumber of molelcules
Total (without water)2,0141
Polymers2,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)10.065, 18.791, 31.424
Angle α, β, γ (deg.)75.16, 88.54, 86.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide PEPTAIBOL GICHIGAMIN


Mass: 2014.454 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tolypocladium sp. Sup5 PDA-1 (fungus)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGICHIGAMIN IS A LINEAR PEPTIDE, MEMBER OF THE PEPTAIBOL FAMILY OF PEPTAIBIOTICS.

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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: 1.48 Å3/Da / Density % sol: 17 %
Crystal growTemperature: 295.65 K / Method: batch mode / Details: 100% METHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.1→25 Å / Num. all: 14245 / Num. obs: 14245 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.253
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 4 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 5.412 / % possible all: 99.6

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SHELXphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.1→25 Å / Num. parameters: 2623 / Num. restraintsaints: 2940 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1206 749 5.25 %RANDOM
obs0.1098 14245 99.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 318 / Occupancy sum non hydrogen: 290
Refinement stepCycle: LAST / Resolution: 1.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms138 0 139 9 286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0202
X-RAY DIFFRACTIONs_angle_d0.0413
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0196
X-RAY DIFFRACTIONs_zero_chiral_vol1.0486
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0789
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0308
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0086
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.093
X-RAY DIFFRACTIONs_approx_iso_adps0.0038

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