[English] 日本語
Yorodumi
- PDB-4h69: Crystal Structure of the Allene Oxide Cyclase 2 from Physcomitrel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h69
TitleCrystal Structure of the Allene Oxide Cyclase 2 from Physcomitrella patens complexed with substrate analog
ComponentsAllene oxide cyclase
KeywordsISOMERASE / B-barrel / Oxylipins / fatty acid / metabolites / allene-oxide cyclase activity
Function / homology
Function and homology information


allene-oxide cyclase / allene-oxide cyclase activity / jasmonic acid biosynthetic process / chloroplast
Similarity search - Function
AOC barrel-like / Allene oxide cyclase-like / Allene oxide cyclase / Allene oxide cyclase superfamily / Allene oxide cyclase / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-10Y / ISOPROPYL ALCOHOL / PHOSPHATE ION / Allene-oxide cyclase
Similarity search - Component
Biological speciesPhyscomitrella patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNeumann, P. / Ficner, R.
CitationJournal: Plant Physiol. / Year: 2012
Title: Crystal Structures of Physcomitrella patens AOC1 and AOC2: Insights into the Enzyme Mechanism and Differences in Substrate Specificity.
Authors: Neumann, P. / Brodhun, F. / Sauer, K. / Herrfurth, C. / Hamberg, M. / Brinkmann, J. / Scholz, J. / Dickmanns, A. / Feussner, I. / Ficner, R.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 4, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Allene oxide cyclase
B: Allene oxide cyclase
C: Allene oxide cyclase
D: Allene oxide cyclase
E: Allene oxide cyclase
F: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,69017
Polymers125,7886
Non-polymers1,90211
Water16,466914
1
A: Allene oxide cyclase
B: Allene oxide cyclase
D: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,14711
Polymers62,8943
Non-polymers1,2548
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-61 kcal/mol
Surface area21960 Å2
MethodPISA
2
C: Allene oxide cyclase
E: Allene oxide cyclase
F: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5436
Polymers62,8943
Non-polymers6493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-36 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.414, 115.570, 87.040
Angle α, β, γ (deg.)90.000, 92.290, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Allene oxide cyclase /


Mass: 20964.643 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: GST-N-terminal fusion / Source: (gene. exp.) Physcomitrella patens (plant) / Gene: aoc2 / Plasmid: pGEX-6-P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8H0N6, allene-oxide cyclase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-10Y / (9Z)-11-{(2R,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid


Mass: 294.429 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H30O3
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 914 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12 % to 14 % (w/v) PEG 4000, 0.25 M (NH4)2SO4, 10 % (w/v) isopropanol and 0.1 M HEPES-KOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE, / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→19.759 Å / Num. all: 90899 / Num. obs: 90899 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 31.916 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.10.5412.554380712378199.9
2.1-2.20.4723.3436188102141100
2.2-2.30.3334.48301358526199.9
2.3-2.40.2675.39252257153199.9
2.4-2.830.1737.447195620514199.8
2.83-3.260.08812.193792411098199.7
3.26-3.690.06615.46216806502199.5
3.69-4.120.05518.26134894086199.3
4.12-4.550.04721.3988942693199.3
4.55-100.04224.34238447075199.6
10-200.02432.032185660199.1

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AOC1 from Physcomytrella patens

Resolution: 2→19.759 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8445 / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): -3 / Phase error: 23.16 / Stereochemistry target values: ML
Details: MEDIUM NCS RESTRAINS HAVE BEEN USED AT THE EARLY STAGES OF REFINEMENT AND HAVE BEEN RELEASED FOR VARIABLE PARTS OF THE AOCS MONOMERS WHERE APPROPRIATE. THE FINAL REFINEMENT STEPS HAVE BEEN ...Details: MEDIUM NCS RESTRAINS HAVE BEEN USED AT THE EARLY STAGES OF REFINEMENT AND HAVE BEEN RELEASED FOR VARIABLE PARTS OF THE AOCS MONOMERS WHERE APPROPRIATE. THE FINAL REFINEMENT STEPS HAVE BEEN APPLIED WITHOUT ANY NCS RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 4546 5 %thin shells (NCS)
Rwork0.1941 ---
obs0.1958 90861 99.75 %-
all-90899 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.564 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 95.96 Å2 / Biso mean: 30.8267 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1-4.3206 Å2-0 Å2-4.5287 Å2
2---1.8111 Å2-0 Å2
3----2.5095 Å2
Refinement stepCycle: LAST / Resolution: 2→19.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8469 0 131 914 9514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058897
X-RAY DIFFRACTIONf_angle_d0.85612057
X-RAY DIFFRACTIONf_chiral_restr0.061306
X-RAY DIFFRACTIONf_plane_restr0.0051585
X-RAY DIFFRACTIONf_dihedral_angle_d12.9253291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.30741510.271728643015100
2.0227-2.04650.32081520.263828833035100
2.0465-2.07140.27641530.249329053058100
2.0714-2.09760.29251510.241928603011100
2.0976-2.12520.26841510.239228773028100
2.1252-2.15420.31291500.238628543004100
2.1542-2.1850.27671510.228228553006100
2.185-2.21760.27671520.216429003052100
2.2176-2.25220.2441490.204528202969100
2.2522-2.2890.25191530.213429113064100
2.289-2.32840.24421500.212128432993100
2.3284-2.37070.26591520.205628983050100
2.3707-2.41620.25461520.210828763028100
2.4162-2.46550.24281500.213828553005100
2.4655-2.5190.25651520.206428873039100
2.519-2.57740.27311510.202428643015100
2.5774-2.64180.2351530.208829163069100
2.6418-2.7130.23341500.200228402990100
2.713-2.79260.20671520.189128873039100
2.7926-2.88250.2381510.19728723023100
2.8825-2.98520.22741520.199128823034100
2.9852-3.10430.21511510.193628813032100
3.1043-3.2450.22961510.196428553006100
3.245-3.41520.21131510.1892882303399
3.4152-3.6280.20021530.18562895304899
3.628-3.90610.19151490.17542843299299
3.9061-4.29550.20511530.15952889304299
4.2955-4.90880.14831520.142428983050100
4.9088-6.15340.20291530.17582896304999
6.1534-19.75950.24181550.20062927308299
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)
11.5716-0.18540.18431.4292-0.15351.74110.02760.0390.0407-0.04960.0441-0.0016-0.1222-0.0728-0.01960.00540.04130.0408-0.01880.00310.013728.74610.202132.0292
21.3356-0.2661-0.20011.97-0.36041.15490.08240.0146-0.0287-0.1383-0.01720.00260.12810.0545-0.04830.0440.02260.0076-0.00650.0053-0.004736.5405-24.113439.1667
31.3525-0.2154-0.38321.65560.04491.1424-0.0016-0.0738-0.00680.0974-0.00120.0092-0.0138-0.02470.01-0.05520.0850.0089-0.1569-0.0643-0.137354.2433-40.946112.8253
41.8062-0.0632-0.36261.85980.09351.5849-0.0128-0.1975-0.10610.23010.02870.32720.0503-0.35430.01030.07570.00660.070.19790.08030.126216.5832-11.718451.691
51.27980.31180.04880.95920.20411.51850.01550.0757-0.1619-0.03060.0616-0.09380.19790.0756-0.05860.11040.0515-0.0528-0.0577-0.0749-0.009660.6324-59.4717-5.509
61.7261-0.0092-0.14471.8225-0.03651.71560.06750.01510.1665-0.04410.0647-0.1975-0.18050.2005-0.0464-0.056-0.0487-0.0221-0.1648-0.0625-0.060373.6386-36.9699-4.8252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-4 - 188
2X-RAY DIFFRACTION2chain BB-4 - 188
3X-RAY DIFFRACTION3chain CC-4 - 188
4X-RAY DIFFRACTION4chain DD-4 - 188
5X-RAY DIFFRACTION5chain EE-4 - 188
6X-RAY DIFFRACTION6chain FF-4 - 188

+
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