[English] 日本語
Yorodumi
- PDB-7d79: The structure of DcsB complex with its substrate analogue -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d79
TitleThe structure of DcsB complex with its substrate analogue
ComponentsDltD domain-containing protein
KeywordsHYDROLASE / Thioesterase / Complex
Function / homology: / Serine aminopeptidase, S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-GY0 / methyl 3-sulfanylpropanoate / DltD domain-containing protein
Function and homology information
Biological speciesBeauveria bassiana
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.10411425302 Å
AuthorsTang, Y. / Zhou, J.H. / Wang, G.Q.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: A Polyketide Cyclase That Forms Medium-Ring Lactones.
Authors: Gao, D.W. / Jamieson, C.S. / Wang, G. / Yan, Y. / Zhou, J. / Houk, K.N. / Tang, Y.
History
DepositionOct 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: DltD domain-containing protein
A: DltD domain-containing protein
B: DltD domain-containing protein
C: DltD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,83919
Polymers140,6934
Non-polymers1,14615
Water10,323573
1
D: DltD domain-containing protein
A: DltD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,16012
Polymers70,3472
Non-polymers81310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-16 kcal/mol
Surface area21520 Å2
MethodPISA
2
C: DltD domain-containing protein
hetero molecules

B: DltD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6797
Polymers70,3472
Non-polymers3335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4790 Å2
ΔGint-45 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.263, 59.011, 113.990
Angle α, β, γ (deg.)84.846, 78.552, 84.008
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 4 molecules DABC

#1: Protein
DltD domain-containing protein / Thioesterase


Mass: 35173.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beauveria bassiana (strain ARSEF 2860) (fungus)
Strain: ARSEF 2860 / Gene: BBA_03809 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: J4WAT9

-
Non-polymers , 7 types, 588 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GY0 / methyl 3-[(E,3R,9R)-3,9-bis(oxidanyl)dec-4-enoyl]sulfanylpropanoate


Mass: 304.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GYF / methyl 3-sulfanylpropanoate


Mass: 120.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MMT, 25% PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 64129 / % possible obs: 92.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.6699461815 Å2 / CC1/2: 0.75 / Net I/σ(I): 9.56
Reflection shellResolution: 2.11→2.15 Å / Num. unique obs: 64129 / CC1/2: 0.734

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.10411425302→39.0031543568 Å / SU ML: 0.265288513473 / Cross valid method: FREE R-VALUE / σ(F): 1.97263301931 / Phase error: 24.2618528783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226936694139 2979 4.98794454491 %
Rwork0.182374770165 56745 -
obs0.184609801223 59724 85.9610236334 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.1019481266 Å2
Refinement stepCycle: LAST / Resolution: 2.10411425302→39.0031543568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8978 0 68 573 9619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00188446566649261
X-RAY DIFFRACTIONf_angle_d0.48935190025112509
X-RAY DIFFRACTIONf_chiral_restr0.04357970862751379
X-RAY DIFFRACTIONf_plane_restr0.00389818491591634
X-RAY DIFFRACTIONf_dihedral_angle_d3.012531370347272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.13860.321349440053890.2426155297571673X-RAY DIFFRACTION53.7686908758
2.1386-2.17550.2533415400621130.2164536925262000X-RAY DIFFRACTION63.5871200722
2.1755-2.2150.2687058398481190.2265060945842190X-RAY DIFFRACTION69.9696969697
2.215-2.25760.3329954083831160.2468695187182371X-RAY DIFFRACTION74.2388059701
2.2576-2.30370.3009265876361350.2172181129152474X-RAY DIFFRACTION80.006133088
2.3037-2.35380.3169919402511230.207945007812715X-RAY DIFFRACTION85.071942446
2.3538-2.40850.254573891741270.2076577332882708X-RAY DIFFRACTION86.7237687366
2.4085-2.46880.269986044071540.2065219788062752X-RAY DIFFRACTION86.1292234736
2.4688-2.53550.249126095511320.2039854230852770X-RAY DIFFRACTION89.3748075146
2.5355-2.61010.2863934872581560.2007106024972998X-RAY DIFFRACTION94.601079784
2.6101-2.69430.2436096214791810.1994336920342932X-RAY DIFFRACTION94.9085365854
2.6943-2.79060.2577414490841660.2036820132942988X-RAY DIFFRACTION93.9529341674
2.7906-2.90230.2397136970991510.1987809438822927X-RAY DIFFRACTION94.3014705882
2.9023-3.03430.2631010443841440.2025240189722940X-RAY DIFFRACTION93.0036188179
3.0343-3.19420.2564093739031240.1946422509592813X-RAY DIFFRACTION88.7311178248
3.1942-3.39430.2200371534321600.1899275160642862X-RAY DIFFRACTION91.216420163
3.3943-3.65620.185548695341580.1745930102413044X-RAY DIFFRACTION96.0696069607
3.6562-4.02380.2092131990151670.1570583053052933X-RAY DIFFRACTION94.7722409049
4.0238-4.60520.1684922861951360.145233194972887X-RAY DIFFRACTION90.7535274692
4.6052-5.7990.1939123812151630.153130658152915X-RAY DIFFRACTION92.8226779252
5.799-5.7990.1861326772311650.1537254710882853X-RAY DIFFRACTION91.3438256659

+
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