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- PDB-4h6a: Crystal Structure of the Allene Oxide Cyclase 2 from Physcomitrel... -

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Basic information

Entry
Database: PDB / ID: 4h6a
TitleCrystal Structure of the Allene Oxide Cyclase 2 from Physcomitrella patens
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
ISOPROPYL ALCOHOL / Allene-oxide cyclase
Similarity search - Component
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)126,77718
Polymers125,7886
Non-polymers98912
Water11,440635
1
A: Allene oxide cyclase
B: Allene oxide cyclase
D: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4079
Polymers62,8943
Non-polymers5136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-97 kcal/mol
Surface area22040 Å2
MethodPISA
2
C: Allene oxide cyclase
E: Allene oxide cyclase
F: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3719
Polymers62,8943
Non-polymers4776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-39 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.589, 115.396, 87.027
Angle α, β, γ (deg.)90.000, 91.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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 subsp. patens (plant)
Gene: aoc2, PHYPADRAFT_158446 / Plasmid: pGEX-6-P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9RB27, allene-oxide cyclase

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Non-polymers , 5 types, 647 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.39 %
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

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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: 1.95→19.5 Å / Num. all: 92382 / Num. obs: 92382 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 36.63 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.98-2.090.5023.24532671324699.9
2.09-2.20.3674.41472321173899.8
2.2-2.30.2616.0433793839199.8
2.3-2.790.14210.631047522592399.8
2.79-3.230.05325.16476351177199.9
3.23-3.670.0340.6327280677799.9
3.67-4.110.02254.5116814422299.8
4.11-4.550.01668.54108842744100
4.55-100.01570.8127485699099.8
10-200.01377.71203358088.5
20-30
30

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AOC1 from Physcomytrella patens

Resolution: 1.95→19.449 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8293 / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): -3 / Phase error: 24.45 / 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
Rfree0.2308 4838 5 %thin shells (NCS)
Rwork0.2 ---
obs0.2015 -99.77 %-
all-96747 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.876 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 136.35 Å2 / Biso mean: 39.2908 Å2 / Biso min: 15 Å2
Baniso -1Baniso -2Baniso -3
1-9.763 Å2-0 Å2-7.3053 Å2
2---3.3121 Å2-0 Å2
3----6.4509 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8457 0 65 635 9157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038727
X-RAY DIFFRACTIONf_angle_d0.79411824
X-RAY DIFFRACTIONf_chiral_restr0.0541280
X-RAY DIFFRACTIONf_plane_restr0.0041546
X-RAY DIFFRACTIONf_dihedral_angle_d12.9343182
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 (%)
1.95-1.97220.34021630.311530773240100
1.9722-1.99530.32121610.279930703231100
1.9953-2.01960.28711610.259730503211100
2.0196-2.04520.30661610.261830643225100
2.0452-2.07210.30471610.25930533214100
2.0721-2.10040.25781610.235530633224100
2.1004-2.13040.24331610.232330573218100
2.1304-2.16210.27271610.246430493210100
2.1621-2.19590.311600.237130573217100
2.1959-2.23180.27961620.218630763238100
2.2318-2.27030.23651610.220130453206100
2.2703-2.31150.28551600.217430383198100
2.3115-2.35590.23591610.218530583219100
2.3559-2.40390.26771620.208830763238100
2.4039-2.4560.27351590.222830283187100
2.456-2.51310.27021620.23230793241100
2.5131-2.57580.26411610.231530473208100
2.5758-2.64530.26691610.223330613222100
2.6453-2.72290.28541620.221230943256100
2.7229-2.81050.24031610.199930513212100
2.8105-2.91070.2511600.198730393199100
2.9107-3.02680.25391630.200130853248100
3.0268-3.1640.21111600.194730493209100
3.164-3.330.22831610.198230663227100
3.33-3.53750.23061640.196431013265100
3.5375-3.80870.22331610.189530553216100
3.8087-4.18860.19781630.162430973260100
4.1886-4.78680.16241610.144130763237100
4.7868-6.00130.17961620.175430923254100
6.0013-19.44960.21111610.20273056321797
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)
11.5316-0.62760.31881.6953-0.16192.48850.0248-0.013-0.00360.00980.0474-0.0066-0.1891-0.1612-0.03090.09420.03970.02340.1018-0.00580.107728.2734-0.017531.942
21.1992-0.38860.04172.3086-0.39921.85790.0657-0.0565-0.0281-0.22470.00210.04370.14740.0153-0.05830.12870.01340.00860.1713-0.00530.172836.7594-24.005239.3778
31.6780.0074-0.94332.12940.02181.80660.0378-0.0081-0.01510.1762-0.01940.056-0.13640.08350.06050.08940.0828-0.01920.0118-0.05030.07853.8715-41.072613.0809
42.0443-0.5455-0.0062.4136-0.76811.9487-0.104-0.3615-0.1860.28150.32310.3135-0.1422-0.49390.00310.1180.0740.1010.39030.12340.200316.8806-11.567252.0804
52.12130.8585-0.20921.14340.89852.1686-0.03890.1231-0.1513-0.00040.1741-0.12630.32290.228-0.01360.18490.1022-0.05270.0102-0.06430.070459.7788-59.5656-5.4772
61.71380.0934-0.37922.1017-0.07532.32770.00510.06490.261-0.17590.0925-0.1789-0.36350.4670.01820.2189-0.1084-0.00420.2158-0.05550.198373.6369-37.372-4.8546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-5 - 188
2X-RAY DIFFRACTION2chain BB-5 - 188
3X-RAY DIFFRACTION3chain CC-5 - 188
4X-RAY DIFFRACTION4chain DD-5 - 188
5X-RAY DIFFRACTION5chain EE-4 - 188
6X-RAY DIFFRACTION6chain FF-4 - 188

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