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- PDB-1w7q: Feglymycin P65 crystal form -

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Basic information

Entry
Database: PDB / ID: 1w7q
TitleFeglymycin P65 crystal form
ComponentsFEGLYMYCIN
KeywordsANTIBIOTIC / ANTIVIRAL / ANTI HIV / ANTIBACTERIAL
Function / homologyFEGLYMYCIN / ETHANOL / :
Function and homology information
Biological speciesSTREPTOMYCES SP. (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 1.1 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 1.3Jul 12, 2017Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Revision 1.4May 30, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,93248
Polymers11,4056
Non-polymers2,52742
Water1,38777
1
A: FEGLYMYCIN
B: FEGLYMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,05723
Polymers3,8022
Non-polymers1,25521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: FEGLYMYCIN
F: FEGLYMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1127
Polymers3,8022
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
D: FEGLYMYCIN
E: FEGLYMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,76318
Polymers3,8022
Non-polymers96116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.544, 83.544, 35.734
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.59017, 0.7284, -0.34803), (0.76397, 0.36462, -0.53236), (-0.26088, -0.58007, -0.77166)-8.30998, 24.46642, 49.15743
2given(0.98557, -0.01927, 0.16816), (-0.0326, 0.95329, 0.30029), (-0.16609, -0.30144, 0.93891)-6.79917, 12.01521, 31.48958
3given(-0.50762, 0.86158, 0.0001), (0.86158, 0.50762, -0.00061), (-0.00057, -0.00023, -1)0.45854, -0.17609, -11.8395
4given(0.92004, -0.16985, 0.3531), (-0.06171, 0.8271, 0.55866), (-0.38694, -0.53577, 0.75048)-2.92988, 31.74117, 59.32485
5given(-0.49292, 0.86257, -0.11404), (0.85133, 0.45108, -0.2679), (-0.17965, -0.22914, -0.95667)-9.64514, 8.34192, 17.25547

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Components

#1: Protein/peptide
FEGLYMYCIN


Type: Polypeptide / Class: Antimicrobial, Antiretroviral / Mass: 1900.854 Da / Num. of mol.: 6 / 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-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FEGLYMYCIN IS A A LINEAR TRIDECAMER PEPTIDE HERE, FEGLYMYCIN IS REPRESENTED BY THE SEQUENCE ...THE FEGLYMYCIN IS A A LINEAR TRIDECAMER PEPTIDE HERE, FEGLYMYCIN IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: FEGLYMYCIN CHAIN: A, B, C, D, E, F COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 13 DESCRIPTION: FEGLYMYCIN IS A LINEAR HELICAL TRIDECAMER PEPTIDE
Nonpolymer detailsEDO - THE PEG8000 USED IN CRYSTALLISATION WAS BUILT IN THE MODEL AS A SERIES OF CONNECTED ETHYLENE ...EDO - THE PEG8000 USED IN CRYSTALLISATION WAS BUILT IN THE MODEL AS A SERIES OF CONNECTED ETHYLENE GLYCOL UNITS

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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: 2.52 Å3/Da / Density % sol: 51.2 % / Description: MEROHEDRAL TWIN, APPARENT SPACE GROUP P6522
Crystal growpH: 8.4 / Details: 0.1 M TRIS/TRISHCL PH=8.4, 4% PEG8000, pH 8.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M06XCE / Wavelength: 1.5418
DetectorType: BRUKER-NONIUS / Detector: CCD / Date: Oct 10, 2002 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.1→72.35 Å / Num. obs: 57985 / % possible obs: 100 % / Redundancy: 9.97 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.31
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 4.64 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.06 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.1→72.35 Å / Num. parameters: 9811 / Num. restraintsaints: 13414 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: TWIN FRACTION 0.51
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2901 5 %THIN SHELLS
all0.1692 57958 --
obs0.1689 -100 %-
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 646 / Occupancy sum non hydrogen: 1026
Refinement stepCycle: LAST / Resolution: 1.1→72.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 122 77 1027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.045
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.292
X-RAY DIFFRACTIONs_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0.092

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