[English] 日本語
Yorodumi
- PDB-7x86: The crystal structure of PloI4-F124L in complex with endo-4+2 adduct -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x86
TitleThe crystal structure of PloI4-F124L in complex with endo-4+2 adduct
ComponentsPloI4
KeywordsLIGASE / PloI4 / mutant / 4+2 Cyclase / endo-4+2 adduct
Function / homologyAOC barrel-like / Allene oxide cyclase-like / Beta Barrel / Mainly Beta / Chem-A3I
Function and homology information
Biological speciesMicromonospora sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsLi, M. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21822705 China
CitationJournal: Nat.Chem. / Year: 2023
Title: A cyclase that catalyses competing 2 + 2 and 4 + 2 cycloadditions.
Authors: Wang, H. / Zou, Y. / Li, M. / Tang, Z. / Wang, J. / Tian, Z. / Strassner, N. / Yang, Q. / Zheng, Q. / Guo, Y. / Liu, W. / Pan, L. / Houk, K.N.
History
DepositionMar 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PloI4
B: PloI4
C: PloI4
D: PloI4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8478
Polymers61,8574
Non-polymers1,9914
Water3,081171
1
A: PloI4
C: PloI4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9244
Polymers30,9282
Non-polymers9952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-26 kcal/mol
Surface area13010 Å2
MethodPISA
2
B: PloI4
D: PloI4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9244
Polymers30,9282
Non-polymers9952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-28 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.980, 88.810, 50.770
Angle α, β, γ (deg.)90.000, 92.730, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
PloI4


Mass: 15464.144 Da / Num. of mol.: 4 / Mutation: F124L
Source method: isolated from a genetically manipulated source
Details: This structure is F124L mutant. / Source: (gene. exp.) Micromonospora sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-A3I / (4S,4aS,6aR,8R,9R,10aS,13S,14aS,18aR,18bR,E)-9-ethyl-4,8,19-trihydroxy-10a,12,13,18a-tetramethyl-2,3,4,4a,6a,7,8,9,10,10a,13,14,18a,18b-tetradecahydro-14a,17-(metheno)benzo[b]naphtho[2,1-h][1]azacyclododecine-16,18(1H,15H)-dione


Mass: 497.666 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H43NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1.6 M Sodium phosphate monobasic, 400 mM Potassium phosphate dibasic, 100 mM Sodium phosphate dibasic/Citric acid (pH 4.2)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→90.39 Å / Num. obs: 35426 / % possible obs: 99.5 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.296 / Net I/σ(I): 6.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1720 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X80

7x80


Resolution: 2.303→90.387 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1709 4.83 %
Rwork0.2118 33693 -
obs0.2138 35402 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.3 Å2 / Biso mean: 56.4254 Å2 / Biso min: 18.6 Å2
Refinement stepCycle: final / Resolution: 2.303→90.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 144 171 4626
Biso mean--63.33 48.94 -
Num. residues----576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3031-2.37090.35781390.3093272198
2.3709-2.44740.33381420.2956275897
2.4474-2.53490.33471540.29082797100
2.5349-2.63640.31611430.27112783100
2.6364-2.75640.28531580.26262804100
2.7564-2.90170.27221340.24342803100
2.9017-3.08350.31941320.23852851100
3.0835-3.32160.2911380.22142810100
3.3216-3.65590.24711330.2059283299
3.6559-4.18490.21491500.19042818100
4.1849-5.27250.20161490.15492836100
5.2725-90.3870.21921370.1933288099
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)
10.359-0.10.68060.41380.06391.41030.64680.68930.7931-0.23570.08130.3498-0.63990.5-0.29510.5889-0.02220.06370.42410.01890.4344-35.9845-2.99455.4442
21.5360.2056-0.33153.18160.02693.0023-0.0981-0.4551-0.06110.4186-0.2522-0.44060.48650.42440.21680.38490.08310.03140.33870.09970.3689-34.392-26.352633.3784
32.14040.04270.80941.67860.34354.993-0.1539-0.04140.0727-0.17640.07340.0477-0.42080.15080.12970.31280.02970.06030.17020.00620.3067-38.7605-17.560321.4684
41.93780.41812.15632.7470.61956.50830.36760.3422-0.00990.0395-0.51520.26130.25180.69860.03610.2216-0.09790.11180.14420.05720.3668-34.9312-15.221315.9663
52.1303-0.96654.24720.4672-1.91668.4682-0.1465-0.2142-0.16190.41950.1242-0.4405-0.2078-0.1283-0.01870.6404-0.05090.07110.2749-0.03310.3246-42.2917-8.393931.8044
60.90830.3795-0.21841.3614-1.17382.40650.04250.0755-0.02150.0707-0.03030.11790.09650.159-0.01140.214-0.0136-0.00930.1738-0.03610.2711-39.3112-13.138717.6868
72.22660.0384-0.21522.0474-0.70483.38790.43750.4933-0.32640.1279-0.27630.0449-0.9106-0.3569-0.14520.3363-0.06720.05390.2014-0.01430.3763-42.5863-10.056616.8517
80.639-0.5465-0.9022.78790.05761.4644-0.2317-0.7148-1.2074-0.14870.06030.1876-0.09760.2214-0.24740.46020.0546-0.01060.31090.17260.5003-37.4624-0.418319.498
91.03390.3189-0.63510.8202-1.55774.01320.243-0.14670.13470.3033-0.33050.2508-0.79290.175-0.12910.3820.03930.0260.26130.01170.3274-43.10117.74422.5589
102.3122-2.27681.96622.8761-0.68363.99810.0901-0.25350.8536-0.7272-0.3246-0.6743-0.9230.88660.5520.6697-0.19740.06940.60140.10340.5737-24.255425.7456-12.8058
112.95270.6529-1.87171.1464-0.89235.2107-0.1166-0.01870.1230.21210.17810.37520.2449-0.0060.01150.40140.01240.00040.1940.00890.3589-40.583115.67096.9768
122.41841.0989-0.98411.7296-1.33976.2372-0.2912-0.0499-0.3789-0.2938-0.0646-0.17080.78620.80040.13670.38930.08170.03010.23510.06660.33-31.280910.70080.8002
133.1276-0.5045-2.75332.03850.12184.7997-0.0422-0.26190.1951-0.11040.0861-0.3166-0.27020.44140.040.3708-0.0098-0.08080.1932-0.02040.3609-33.743211.441810.5218
141.55540.3041-3.30640.0829-0.80598.261-0.26660.0447-0.0719-0.79210.29150.04410.32820.03140.04510.76010.0061-0.02760.1891-0.07640.4156-39.8994.6751-6.0036
151.16670.0764-0.83371.8512-0.27631.4389-0.0845-0.13620.0593-0.1378-0.02450.1838-0.24420.17560.04190.40480.0278-0.01750.2131-0.00780.3163-38.12919.19918.4954
161.5925-0.37910.01654.82-0.76664.19180.25690.00690.04220.0017-0.01140.46830.7275-0.3891-0.04470.3242-0.0053-0.00290.19820.02430.3476-40.94126.65289.1758
170.60261.59181.96294.58655.7727.28780.5185-0.3488-0.3719-0.08980.214-0.70060.02640.4064-0.64020.5409-0.11060.06321.314-0.05630.7521-12.1062-20.06067.8149
180.6591-0.7333-1.56382.83511.05753.91040.30070.50850.2090.4069-0.4807-0.71830.6377-0.108-0.1850.4083-0.0361-0.06821.1163-0.0070.5061-13.3295-15.779430.0421
195.4781-0.1408-0.39714.73741.25335.19470.2004-1.22330.04370.7047-0.19520.1204-0.55760.07330.15960.37510.03310.01890.5716-0.02780.3834-36.0215-17.503542.5926
205.4622.5464-3.19931.6576-1.68562.62520.39020.37970.21160.0455-0.2534-0.2137-0.38980.7853-0.09740.33370.0080.04410.92490.11490.4949-14.6156-14.595325.2888
213.24981.0825-2.81166.3858-2.4625.00940.5529-0.48380.35370.2867-0.69280.83820.21310.6036-0.02390.22120.0298-0.0560.3822-0.06830.3194-24.6241-21.850424.7703
222.00770.4227-0.41452.6364-1.06494.47030.0727-0.0432-0.14970.3636-0.0403-0.1483-0.1651.084-0.04530.30140.0845-0.00440.64270.01570.357-19.4498-19.282417.6923
230.5167-0.95710.96884.4905-1.34117.30370.0641-0.3884-0.42210.0346-0.4147-0.74911.33531.2312-0.10980.21050.0199-0.04071.08990.15810.5046-11.3225-21.466324.7692
240.1322-0.7762-0.14184.50050.85080.153-0.2114-0.40890.1390.7845-0.04230.9241-0.3545-0.00130.14650.7314-0.1203-0.00391.7150.05120.6729-14.693114.884124.1249
253.748-0.73030.3241.5557-0.16412.9159-0.01730.6448-0.2605-0.3751-0.0421-0.22350.16780.87060.01010.53740.01070.12550.5391-0.0040.4182-23.924213.0314-10.3281
263.5409-2.02472.59292.8667-0.63184.55290.2717-0.0752-0.35370.0312-0.08650.15990.21310.7503-0.20750.3418-0.09330.05380.64820.03880.3395-16.320113.4563.2169
271.7572-0.6060.94922.47420.31472.1639-0.0314-0.00580.0973-0.0397-0.1311-0.19830.00610.96410.10470.3586-0.05320.0150.71470.05780.4441-15.322216.11368.3256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 40 )A12 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 83 )A41 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 96 )A84 - 96
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 103 )A97 - 103
6X-RAY DIFFRACTION6chain 'A' and (resid 104 through 133 )A104 - 133
7X-RAY DIFFRACTION7chain 'A' and (resid 134 through 145 )A134 - 145
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 11 )B2 - 11
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 21 )B12 - 21
10X-RAY DIFFRACTION10chain 'B' and (resid 22 through 40 )B22 - 40
11X-RAY DIFFRACTION11chain 'B' and (resid 41 through 67 )B41 - 67
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 83 )B68 - 83
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 96 )B84 - 96
14X-RAY DIFFRACTION14chain 'B' and (resid 97 through 103 )B97 - 103
15X-RAY DIFFRACTION15chain 'B' and (resid 104 through 133 )B104 - 133
16X-RAY DIFFRACTION16chain 'B' and (resid 134 through 145 )B134 - 145
17X-RAY DIFFRACTION17chain 'C' and (resid 4 through 11 )C4 - 11
18X-RAY DIFFRACTION18chain 'C' and (resid 12 through 21 )C12 - 21
19X-RAY DIFFRACTION19chain 'C' and (resid 22 through 40 )C22 - 40
20X-RAY DIFFRACTION20chain 'C' and (resid 41 through 67 )C41 - 67
21X-RAY DIFFRACTION21chain 'C' and (resid 68 through 83 )C68 - 83
22X-RAY DIFFRACTION22chain 'C' and (resid 84 through 124 )C84 - 124
23X-RAY DIFFRACTION23chain 'C' and (resid 125 through 145 )C125 - 145
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 11 )D1 - 11
25X-RAY DIFFRACTION25chain 'D' and (resid 12 through 40 )D12 - 40
26X-RAY DIFFRACTION26chain 'D' and (resid 41 through 83 )D41 - 83
27X-RAY DIFFRACTION27chain 'D' and (resid 84 through 145 )D84 - 145

+
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