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- PDB-4h6b: Structural basis for allene oxide cyclization in moss -

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Basic information

Entry
Database: PDB / ID: 4h6b
TitleStructural basis for allene oxide cyclization in moss
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
Allene oxide cyclase / Allene oxide cyclase superfamily / Allene oxide cyclase / AOC barrel-like / Allene oxide cyclase-like / Allene oxide cyclase/Dirigent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-10X / Chem-10Y / HEXANE-1,6-DIOL / PHOSPHATE ION / allene-oxide cyclase
Similarity search - Component
Biological speciesPhyscomitrella patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allene oxide cyclase
D: Allene oxide cyclase
C: Allene oxide cyclase
B: Allene oxide cyclase
E: Allene oxide cyclase
F: Allene oxide cyclase
G: Allene oxide cyclase
H: Allene oxide cyclase
I: Allene oxide cyclase
J: Allene oxide cyclase
K: Allene oxide cyclase
L: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,97750
Polymers253,13912
Non-polymers4,83838
Water46,3172571
1
A: Allene oxide cyclase
D: Allene oxide cyclase
C: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,58512
Polymers63,2853
Non-polymers1,3009
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-72 kcal/mol
Surface area21640 Å2
MethodPISA
2
B: Allene oxide cyclase
E: Allene oxide cyclase
F: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,74015
Polymers63,2853
Non-polymers1,45512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-71 kcal/mol
Surface area21600 Å2
MethodPISA
3
G: Allene oxide cyclase
H: Allene oxide cyclase
I: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,38512
Polymers63,2853
Non-polymers1,1019
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-77 kcal/mol
Surface area21850 Å2
MethodPISA
4
J: Allene oxide cyclase
K: Allene oxide cyclase
L: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,26711
Polymers63,2853
Non-polymers9828
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-84 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.420, 67.513, 161.879
Angle α, β, γ (deg.)84.36, 79.15, 62.13
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ADCBEFGHIJKL

#1: Protein
Allene oxide cyclase


Mass: 21094.898 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: GST N-terminal fusion / Source: (gene. exp.) Physcomitrella patens (plant) / Gene: aoc, aoc1 / Plasmid: pGEX-6-P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GS38, allene-oxide cyclase

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Non-polymers , 5 types, 2609 molecules

#2: Chemical ChemComp-10X / (9Z)-11-{(2S,3S)-3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}undec-9-enoic acid


Mass: 294.429 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H30O3
#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.: 2 / Source method: obtained synthetically / Formula: C18H30O3
#4: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2571 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 292 K / pH: 4.2
Details: Hampton Magic Screen condition no. 49 containing 20 % (w/v) PEG 8000, 0.1 M Na3PO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
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: 1.35→19.85 Å / Num. obs: 505495 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 23.15 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 15.1
Reflection shellResolution: 1.35→1.45 Å / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.1 / % possible all: 84.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DIO

2dio


Resolution: 1.35→19.85 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.09 / SU R Cruickshank DPI: 0.0513 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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
Rfree0.169 25280 5 %THIN SHELLS (NCS)
Rwork0.141 ---
obs0.143 480301 92.8 %-
all-505495 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20.95 Å20.48 Å2
2---0.11 Å2-0.34 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16824 0 300 2571 19695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0217917
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9824359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29152215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.43224.036778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.546152693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6791552
X-RAY DIFFRACTIONr_chiral_restr0.0790.22534
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113960
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr9.371317917
X-RAY DIFFRACTIONr_sphericity_free28.89752571
X-RAY DIFFRACTIONr_sphericity_bonded19.957517401
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 1428 -
Rwork0.267 27129 -
obs--71.23 %

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