[English] 日本語
Yorodumi
- PDB-1w7q: Feglymycin P65 crystal form -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein/peptide
FEGLYMYCIN


Type: PolypeptidePeptide / Class: Antimicrobial, AntiretroviralManagement of HIV/AIDS / 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 / Ethanol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more