[English] 日本語
Yorodumi
- PDB-7w6d: Polyketide cyclase OAC-F24I mutant from Cannabis sativa in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w6d
TitlePolyketide cyclase OAC-F24I mutant from Cannabis sativa in complex with olivetolic acid
ComponentsOlivetolic acid cyclase
KeywordsLYASE / olivetolic acid cyclase / polypeptide cyclase
Function / homology
Function and homology information


olivetolic acid cyclase / olivetolic acid biosynthetic process / pollen tube adhesion / cannabinoid biosynthetic process / cyclase activity / terpenoid biosynthetic process / lyase activity / metal ion binding / cytoplasm
Similarity search - Function
Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Dimeric alpha-beta barrel
Similarity search - Domain/homology
2,4-bis(oxidanyl)-6-pentyl-benzoic acid / Olivetolic acid cyclase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsNakashima, Y. / Lee, Y.E. / Morita, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Org.Lett. / Year: 2022
Title: Dual Engineering of Olivetolic Acid Cyclase and Tetraketide Synthase to Generate Longer Alkyl-Chain Olivetolic Acid Analogs.
Authors: Lee, Y.E. / Nakashima, Y. / Kodama, T. / Chen, X. / Morita, H.
History
DepositionDec 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: Olivetolic acid cyclase
B: Olivetolic acid cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8404
Polymers24,3922
Non-polymers4492
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-10 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.795, 39.431, 43.412
Angle α, β, γ (deg.)70.379, 75.480, 67.777
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Olivetolic acid cyclase


Mass: 12195.995 Da / Num. of mol.: 2 / Mutation: F24I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Gene: OAC / Production host: Escherichia coli M15 (bacteria) / References: UniProt: I6WU39, olivetolic acid cyclase
#2: Chemical ChemComp-4MX / 2,4-bis(oxidanyl)-6-pentyl-benzoic acid


Mass: 224.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES-NaOH pH 6.5, 30% PEG3350, 1.2% 1,3-butanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.54→40.48 Å / Num. obs: 51358 / % possible obs: 95.4 % / Redundancy: 4 % / Biso Wilson estimate: 13.51 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 7 / Num. unique obs: 1259 / CC1/2: 0.975 / Rrim(I) all: 0.2 / % possible all: 90.6

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B08

5b08


Resolution: 1.54→40.48 Å / SU ML: 0.1308 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 17.3014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.176 2429 4.73 %
Rwork0.1519 48929 -
obs0.153 51358 92.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.27 Å2
Refinement stepCycle: LAST / Resolution: 1.54→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 247 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062041
X-RAY DIFFRACTIONf_angle_d0.9182802
X-RAY DIFFRACTIONf_chiral_restr0.0614298
X-RAY DIFFRACTIONf_plane_restr0.0057359
X-RAY DIFFRACTIONf_dihedral_angle_d21.5531753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.17411370.19712787X-RAY DIFFRACTION89.09
1.57-1.610.23561270.19332877X-RAY DIFFRACTION93.12
1.61-1.640.21581160.18392985X-RAY DIFFRACTION92.9
1.64-1.680.22631330.1872873X-RAY DIFFRACTION93.07
1.68-1.730.17961520.18042933X-RAY DIFFRACTION93.15
1.73-1.780.20441660.18182833X-RAY DIFFRACTION93.08
1.78-1.840.22441360.17612950X-RAY DIFFRACTION93.97
1.84-1.90.18111410.17332826X-RAY DIFFRACTION91.63
1.9-1.980.21511370.16222924X-RAY DIFFRACTION93.55
1.98-2.070.16681560.15392947X-RAY DIFFRACTION93.18
2.07-2.180.18351490.1532891X-RAY DIFFRACTION93.42
2.18-2.320.20031370.15022917X-RAY DIFFRACTION93.62
2.32-2.490.17151710.14822837X-RAY DIFFRACTION92.33
2.49-2.750.1551520.14652806X-RAY DIFFRACTION90.62
2.75-3.140.1711470.14442879X-RAY DIFFRACTION92.2
3.14-3.960.17671380.12472842X-RAY DIFFRACTION91.13
3.96-40.480.1371340.1392822X-RAY DIFFRACTION90.95
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)
10.0134748845368-0.02408734337260.03597920852390.0552229437278-0.08394590835530.1231492522070.1589497934230.343967923735-0.04897366054340.217699255898-0.1522144549680.118625121652-0.381991978534-0.2903638811850.001341242325710.133239447566-0.00611653007018-0.01666157713010.161500425545-0.02993438816840.18614240581733.12099225484.861383922996.19739784456
20.508267177855-0.2574076777110.1937449547850.354835413689-0.0983467258370.1194743614220.190990147630.09638383685920.208463989602-0.15890274875-0.0709172255671-0.00443665213650.01159190715080.01104805369380.03777052211770.0598825357486-0.002606142275820.01248732711110.07180165099980.01228030994640.10619767101412.039426536912.303463460710.9316691944
30.4328506318260.263525871514-0.5535755992480.523449834503-0.3480190609740.8999265073140.05305806408-0.0313359065570.1669955536710.1884601932520.000407267720930.0379698035754-0.07961683873270.0272326448190.02595817028590.103320105320.01611373775480.01296985669150.0888435394542-0.01969027145570.08428746410559.3314816117413.203400039322.9045692221
40.790759531518-0.363614895309-0.3188746521990.9844311890160.1332577883291.14444711206-0.204012923938-0.198050743145-0.01480208710370.0956992205029-0.0838786658782-0.3152306608630.3233987707480.440046622757-0.2414946449840.1507054466130.07006608474970.003498040927290.1678504713360.03150369996880.064535318837721.9816888922.1774638747419.3113728765
50.3262017802440.219271842282-0.403888748730.45621354803-0.2418510299751.081859687420.1413168890750.148320220040.03303445840760.141195650689-0.005343691783880.28190373021-0.2119786954960.04403299638010.03295064466090.09976988635720.01328871721710.01246745476810.0847114480994-0.009625255298020.25091955380910.593271330420.894006288210.3640297149
60.3173845536880.325892374983-0.1057375874380.2757750070090.008657710535940.1325515009230.103146822275-0.0700824434340.0425793838035-0.159711147761-0.102365171261-0.004574247253420.005106168672970.0829195326708-0.001863423859510.07436922518220.01796308316180.007966344277360.0881901382610.006947395143150.10720470177319.114274940210.282934073712.1126109125
70.578396944776-0.0620473138831-0.1420836058850.78307376170.1136485381260.657779597677-0.04606432758090.0181397059870.032093812938-0.0544495487053-0.009456294674860.03422732966170.1422716818670.00712714266706-0.04242161627350.05577490124990.00632372969793-0.01004429227780.05703315151840.002342591294850.069745171081612.07764108524.934644532212.4652533161
80.289037271799-0.26288489684-0.3740099887550.726763479254-0.1352610009880.392942423967-0.008286693696420.07174281811010.02185089272810.01713819382830.08746890919010.1071267340990.08610607087850.1233045645120.007233430919810.0730728884185-0.0187863320279-0.0111021523580.09004249447850.02001518742890.092783600696815.930297086819.0388750969-0.270098781756
90.1447175629930.0284845402708-0.3057179264550.849776503305-0.2462358789470.6922997836740.04507790753620.0450739354495-0.0845805507438-0.1081502601890.1915772703-0.4048039367350.002625631569360.2407955656360.0341149163740.127436173986-0.00655518644013-0.005184800183530.111838413068-0.02004369577150.11099023991423.880155253222.0897527901-7.87324125147
100.1892269262640.0703349437137-0.2185577235570.265801321613-0.1818009338660.15881698582-0.068919381880.0181071717170.0258463210793-0.0608127730980.0370773740234-0.03997034522080.0915894884146-0.1165564390340.0004530115913120.0910217424088-0.0109070521719-0.01352875616840.08117051234780.002738404489240.10933084093713.57416309568.741663955030.174675353941
110.8764147180740.3493765967650.238742839841.10167323546-0.06457175308420.5939712390610.04214757120220.002598107871290.00171384084-0.0299274417395-0.01012167710170.0321333837121-0.088285765481-0.0459843268370.02745414443570.0650865441177-0.009830891215780.007764458925370.07874969486530.004009422170610.053720903355916.990713850725.6499469918-0.487803917314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 2 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 11 )
3X-RAY DIFFRACTION3chain 'A' and (resid 12 through 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 38 )
5X-RAY DIFFRACTION5chain 'A' and (resid 39 through 56 )
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 65 )
7X-RAY DIFFRACTION7chain 'A' and (resid 66 through 101 )
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 16 )
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 39 )
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 56 )
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 101 )

+
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