[English] 日本語
Yorodumi
- PDB-3qit: Thioesterase Domain From Curacin Biosynthetic Pathway -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qit
TitleThioesterase Domain From Curacin Biosynthetic Pathway
ComponentsPolyketide synthase
KeywordsHYDROLASE / Thioesterase / Alpha/Beta Hydrolase / Decarboxylase / Sulfate elimination / Terminal Alkene Production
Function / homology
Function and homology information


phosphopantetheine binding / transferase activity
Similarity search - Function
: / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...: / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Epoxide hydrolase-like / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLyngbya majuscula 19L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsGehret, J.J. / Smith, J.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Terminal Alkene Formation by the Thioesterase of Curacin A Biosynthesis: STRUCTURE OF A DECARBOXYLATING THIOESTERASE.
Authors: Gehret, J.J. / Gu, L. / Gerwick, W.H. / Wipf, P. / Sherman, D.H. / Smith, J.L.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyketide synthase
B: Polyketide synthase
C: Polyketide synthase
D: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)125,5164
Polymers125,5164
Non-polymers00
Water21,6721203
1
A: Polyketide synthase
B: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)62,7582
Polymers62,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-26 kcal/mol
Surface area24110 Å2
MethodPISA
2
C: Polyketide synthase
D: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)62,7582
Polymers62,7582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-26 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.560, 86.911, 87.592
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Polyketide synthase / / CurM TE


Mass: 31379.043 Da / Num. of mol.: 4 / Fragment: Thioesterase domain (UNP residues 1929-2211)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyngbya majuscula 19L (bacteria) / Gene: curM / Plasmid: pMOCR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D0E8E2, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1203 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 27% PEG3350, 0.1 M Tris, 0.2 M sodium chloride, 2.5% glycerol, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2009
Details: K-B PAIR OF BIOMORPH MIRRORS FOR VERTICAL AND HORIZONTAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. all: 114584 / Num. obs: 114584 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 25.1 Å2 / Rsym value: 0.059 / Net I/σ(I): 18.1
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.384 / % possible all: 49.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.68→39.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.456 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 5806 5.1 %RANDOM
Rwork0.16418 ---
all0.16643 108718 --
obs0.16643 108718 90.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20.1 Å2
2---0.29 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.68→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8617 0 0 1203 9820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229035
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.97612347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.08251194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33124.324370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.306151587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4921555
X-RAY DIFFRACTIONr_chiral_restr0.090.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216759
X-RAY DIFFRACTIONr_mcbond_it2.5513.55707
X-RAY DIFFRACTIONr_mcangle_it3.79159268
X-RAY DIFFRACTIONr_scbond_it3.5043.53328
X-RAY DIFFRACTIONr_scangle_it5.13453035
LS refinement shellResolution: 1.681→1.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 233 -
Rwork0.358 4163 -
obs--47.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)Origin x (Å)Origin y (Å)Origin z (Å)
10.5394-0.202-0.12840.76210.13660.6644-0.01430.0189-0.0443-0.0078-0.01340.10850.04-0.09320.02770.0084-0.00640.00970.01880.00130.039931.785444.216342.5338
22.6120.04131.70110.7250.08322.2491-0.03940.10820.1131-0.0075-0.01450.0367-0.18610.03750.05380.0320.00620.00360.0070.00370.043631.914359.64941.4239
31.3252.8943-1.96156.9453-4.23353.89570.03340.0677-0.01910.13550.00190.1437-0.23780.1833-0.03530.0459-0.06880.0240.1407-0.0470.081359.302350.406538.3809
40.544-0.27670.32421.1532-0.25030.5062-0.0405-0.0042-0.03240.11420.0298-0.0948-0.014-0.00280.01070.0307-0.0032-0.00280.01150.00570.027245.558342.211551.8337
50.4309-0.1497-0.08331.4207-0.10780.2981-0.0353-0.04020.08950.12710.02160.004-0.0931-0.02640.01370.050.0203-0.00930.0157-0.00650.029732.904962.553752.3592
60.75760.3815-0.19780.7586-0.15840.58090.0543-0.02640.00220.0339-0.0517-0.07630.03850.0779-0.00260.01120.01040.00350.04840.00670.03861.260646.675718.0805
70.9334-0.5639-0.62543.0571.5410.91720.0929-0.0039-0.0547-0.0731-0.0159-0.232-0.0724-0.0073-0.0770.08340.04070.00430.02540.01310.046436.004358.730624.4202
81.34470.24350.28140.7269-0.55161.22640.03830.0694-0.0093-0.1053-0.0020.10010.05310.0891-0.03630.03750.0203-0.02820.0429-0.00810.024945.904744.16873.9724
948.486620.947318.49839.86998.85817.97580.46110.7577-0.78330.74070.0351-0.44090.74690.0319-0.49620.6472-0.0196-0.20980.1375-0.04280.615447.506758.165723.9936
101.03250.6185-0.12.39580.3561.35510.05880.02870.2257-0.09040.00180.0457-0.26080.049-0.06060.0539-0.00260.02690.02620.0290.076663.506664.513213.4296
112.1032-0.98722.29070.4911-0.9476.604-0.36430.1580.42250.1954-0.057-0.1994-0.46910.17080.42130.15570.0174-0.12270.03460.01010.125881.370224.906824.6483
121.5274-0.6691.06520.4777-0.73491.2223-0.1481-0.0661-0.04390.07060.10060.0098-0.1199-0.11410.04750.04890.0364-0.02660.0695-0.00270.063278.61412.323125.9396
131.36610.4402-0.66611.38920.03130.3741-0.046-0.08090.15450.30410.09220.17170.07550.0505-0.04620.2410.1987-0.00860.2011-0.05210.067766.967922.747539.56
1431.773511.29588.911431.74849.917947.04571.3572-2.04030.30331.2473-0.39030.2821-0.9314-0.762-0.96690.4756-0.13020.16580.46120.07010.276661.6912.135428.6437
151.132-0.77591.27922.9366-0.6093.07480.0545-0.2522-0.30670.02950.18960.23110.2038-0.3534-0.2440.0201-0.0117-0.0070.07030.07180.123378.2973-2.448132.4495
160.33460.34790.14460.56920.1910.72670.030.0016-0.0420.0325-0.0016-0.01630.0006-0.0566-0.02840.00710.0139-0.00590.0438-0.00420.039551.920718.16254.0126
170.9693-1.54452.92235.8951-4.81598.83740.1246-0.0466-0.04610.12950.0521-0.10910.3607-0.1642-0.17670.06550.0325-0.00160.1887-0.01350.121676.519413.87244.0091
182.73370.8862-0.5111.23860.42191.0432-0.0270.10350.0289-0.18420.0635-0.148-0.1075-0.0446-0.03650.03480.00150.02870.0363-0.00710.033964.075423.5629-13.5386
194.16750.43190.38870.6966-1.85675.57540.0367-0.042-0.4212-0.1043-0.0254-0.06350.31590.1117-0.01140.05430.03970.01340.0824-0.04450.130569.345819.5334-1.3224
200.94180.05140.19421.1140.10231.16770.03490.004-0.1894-0.01230.0723-0.06940.2256-0.0701-0.10710.0453-0.0132-0.02140.0192-0.010.054948.42242.1773-1.5273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 106
2X-RAY DIFFRACTION2A107 - 131
3X-RAY DIFFRACTION3A134 - 153
4X-RAY DIFFRACTION4A154 - 220
5X-RAY DIFFRACTION5A221 - 282
6X-RAY DIFFRACTION6B-1 - 130
7X-RAY DIFFRACTION7B131 - 153
8X-RAY DIFFRACTION8B154 - 204
9X-RAY DIFFRACTION9B207 - 215
10X-RAY DIFFRACTION10B216 - 283
11X-RAY DIFFRACTION11C-1 - 15
12X-RAY DIFFRACTION12C16 - 146
13X-RAY DIFFRACTION13C147 - 203
14X-RAY DIFFRACTION14C204 - 215
15X-RAY DIFFRACTION15C216 - 282
16X-RAY DIFFRACTION16D-1 - 138
17X-RAY DIFFRACTION17D139 - 156
18X-RAY DIFFRACTION18D157 - 194
19X-RAY DIFFRACTION19D195 - 206
20X-RAY DIFFRACTION20D215 - 283

+
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