[English] 日本語
Yorodumi
- PDB-2xem: Induced-fit and allosteric effects upon polyene binding revealed ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xem
TitleInduced-fit and allosteric effects upon polyene binding revealed by crystal structures of the Dynemicin thioesterase
ComponentsDYNE7
KeywordsBIOSYNTHETIC PROTEIN / POLYKETIDE BIOSYNTHESIS / ENEDIYNE ANTITUMOR AGENT / THIOESTERASE
Function / homologyThioesterase-like superfamily / thiolester hydrolase activity / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Chem-SSV / DynE7
Function and homology information
Biological speciesMICROMONOSPORA CHERSINA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiew, C.W. / Sharff, A. / Kotaka, M. / Kong, R. / Bricogne, G. / Liang, Z.X. / Lescar, J.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Induced-Fit Upon Ligand Binding Revealed by Crystal Structures of the Hot-Dog Fold Thioesterase in Dynemicin Biosynthesis.
Authors: Liew, C.W. / Sharff, A. / Kotaka, M. / Kong, R. / Sun, H. / Qureshi, I. / Bricogne, G. / Liang, Z.X. / Lescar, J.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Structure and Catalytic Mechanism of the Thioesterase Cale7 in Enediyne Biosynthesis.
Authors: Kotaka, M. / Kong, R. / Qureshi, I. / Ho, Q.S. / Sun, H. / Liew, C.W. / Goh, L.P. / Cheung, P. / Mu, Y. / Lescar, J. / Liang, Z.
History
DepositionMay 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DYNE7
B: DYNE7
C: DYNE7
D: DYNE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9635
Polymers67,7494
Non-polymers2141
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-60.3 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.471, 65.387, 94.411
Angle α, β, γ (deg.)90.00, 99.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
DYNE7 / TEBC


Mass: 16937.232 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROMONOSPORA CHERSINA (bacteria) / Plasmid: PCDF-2 LIC/EK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84HI7
#2: Chemical ChemComp-SSV / (3E,5E,7E,9E,11E,13E)-pentadeca-3,5,7,9,11,13-hexaen-2-one


Mass: 214.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7.5 / Details: PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 39917 / % possible obs: 97.3 % / Observed criterion σ(I): 2.4 / Redundancy: 3.7 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7
Reflection shellResolution: 2.1→6.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 97

-
Processing

Software
NameVersionClassification
BUSTER2.11.0refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W3X

2w3x


Resolution: 2.1→14.84 Å / Cor.coef. Fo:Fc: 0.9547 / Cor.coef. Fo:Fc free: 0.9432 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.184 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.146 / Details: IDEAL-DISTANCE CONTACT TERM SETUP.
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2008 5.05 %RANDOM
Rwork0.161 ---
obs0.1627 39774 96.88 %-
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.1493 Å20 Å21.1108 Å2
2--0.9944 Å20 Å2
3---0.1549 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 2.1→14.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4447 0 16 546 5009
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014614HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936275HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1529SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes738HARMONIC5
X-RAY DIFFRACTIONt_it4614HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.79
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion554SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5387SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2533 169 5.83 %
Rwork0.1936 2731 -
all0.197 2900 -
obs--96.88 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodOrigin x (Å)Origin y (Å)Origin z (Å)L11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)
1refined-7.775911.69823.8792
2refined19.7641-3.895225.63211.0323-0.4402-0.16262.3269-0.14352.10310.02180.03170.1645-0.0083-0.0083-0.0434-0.3311-0.0572-0.0135-0.07160.01750.0226-0.05260.019-0.0451
3refined-2.7036-3.32639.53641.90290.71850.22920.56330.17871.1845-0.0083-0.1024-0.10760.0129-0.0229-0.05320.05010.11730.0312-0.0770.02620.0213-0.02730.0123-0.0041
41.1377-0.0419-0.39621.6051-0.48891.4290.0146-0.1445-0.10350.1126-0.02770.02870.09650.00170.0131-0.05050.01280.0202-0.0260.0144-0.0626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN B)
2X-RAY DIFFRACTION2(CHAIN C)
3X-RAY DIFFRACTION3(CHAIN D)

+
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://pdbjlvh1.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