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- PDB-1w7r: Feglymycin P64 crystal form -

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Basic information

Entry
Database: PDB / ID: 1w7r
TitleFeglymycin P64 crystal form
ComponentsFEGLYMYCIN
KeywordsANTIBIOTIC / ANTIVIRAL / ANTI HIV / ANTIBACTERIAL
Function / homologyFEGLYMYCIN / CITRATE ANION / ISOPROPYL ALCOHOL / :
Function and homology information
Biological speciesSTREPTOMYCES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBunkoczi, G. / Vertesy, L. / Sheldrick, G.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2005
Title: The Antiviral Antibiotic Feglymycin: First Direct Methods Solution of a 1000Plus Equal-Atom Structure
Authors: Bunkoczi, G. / Vertesy, L. / Sheldrick, G.M.
History
DepositionSep 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: FEGLYMYCIN
B: FEGLYMYCIN
C: FEGLYMYCIN
D: FEGLYMYCIN
E: FEGLYMYCIN
F: FEGLYMYCIN
G: FEGLYMYCIN
H: FEGLYMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,63613
Polymers15,2078
Non-polymers4295
Water1,946108
1
A: FEGLYMYCIN
B: FEGLYMYCIN
hetero molecules


  • defined by author&software
  • 3.92 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)3,9224
Polymers3,8022
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: FEGLYMYCIN
D: FEGLYMYCIN


Theoretical massNumber of molelcules
Total (without water)3,8022
Polymers3,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: FEGLYMYCIN
F: FEGLYMYCIN
hetero molecules


  • defined by author&software
  • 3.86 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)3,8623
Polymers3,8022
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: FEGLYMYCIN
H: FEGLYMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0514
Polymers3,8022
Non-polymers2492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.302, 60.302, 83.748
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11E-1014-

IPA

21G-2005-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.47543, -0.8592, 0.18904), (-0.85646, 0.40291, -0.32272), (0.20112, -0.31533, -0.92742)71.12147, 63.91256, 89.63326
2given(-0.51333, -0.85817, 0.00602), (-0.85819, 0.51333, -0.00186), (-0.00149, -0.00612, -0.99998)90.44758, 51.68124, 112.91914
3given(0.98249, -0.01332, -0.18583), (0.07535, 0.94063, 0.33096), (0.17039, -0.33916, 0.92517)4.30107, -29.06056, -12.78037
4given(0.99999, -0.00339, -0.00422), (-0.00338, -0.99999, 0.00299), (-0.00423, -0.00298, -0.99999)30.40956, 52.207, 100.71734
5given(-0.48992, 0.8513, -0.18778), (-0.84666, -0.41332, 0.33518), (0.20772, 0.3232, 0.92325)31.36315, 26.29792, -14.2167
6given(-0.50864, 0.86098, -0.00242), (-0.86098, -0.50863, 0.00444), (0.00259, 0.00435, 0.99999)30.54228, 52.14656, 11.92241
7given(0.98244, 0.02557, 0.1848), (0.08372, -0.94564, -0.31426), (0.16672, 0.32422, -0.93117)14.17619, 54.93308, 68.47797

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Components

#1: Protein/peptide
FEGLYMYCIN


Type: Polypeptide / Class: Antimicrobial, Antiretroviral / Mass: 1900.854 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) STREPTOMYCES SP. (bacteria) / References: NOR: NOR01081, FEGLYMYCIN
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFEGLYMYCIN IS A LINEAR TRIDECAMER PEPTIDE. HERE, FEGLYMYCIN IS REPRESENTED BY THE SEQUENCE (SEQRES) ...FEGLYMYCIN IS A LINEAR TRIDECAMER PEPTIDE. HERE, FEGLYMYCIN IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: FEGLYMYCIN CHAIN: A, B, C, D, E, F, G, H COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 13 DESCRIPTION: FEGLYMYCIN IS A LINEAR HELICAL TRIDECAMER PEPTIDE

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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: 2.6 Å3/Da / Density % sol: 52.6 %
Description: MEROHEDRALLY TWINNED, APPARENT SPACE GROUP P6422
Crystal growpH: 6.5
Details: 0.25 M NA3CIT/H3CIT PH=6.5 30% ISOPROPANOL, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2003 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→28.37 Å / Num. obs: 34149 / % possible obs: 99.8 % / Redundancy: 14.17 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.5
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 10.95 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.49 / % possible all: 99.1

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
SADABSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W7Q

1w7q


Resolution: 1.4→28.4 Å / Num. parameters: 11147 / Num. restraintsaints: 14594 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: TWIN FRACTION 0.50
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1695 5 %THIN SHELLS
all0.1749 33976 --
obs0.1739 -99.8 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 676 / Occupancy sum non hydrogen: 1221
Refinement stepCycle: LAST / Resolution: 1.4→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 21 108 1233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.294
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.096

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