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- PDB-4h6c: Crystal Structure of the Allene Oxide Cyclase 1 from Physcomitrel... -

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Basic information

Entry
Database: PDB / ID: 4h6c
TitleCrystal Structure of the Allene Oxide Cyclase 1 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 / Allene oxide cyclase/Dirigent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
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)255,46235
Polymers253,13912
Non-polymers2,32423
Water46,6772591
1
A: Allene oxide cyclase
D: Allene oxide cyclase
C: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8068
Polymers63,2853
Non-polymers5215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-61 kcal/mol
Surface area21360 Å2
MethodPISA
2
B: Allene oxide cyclase
E: Allene oxide cyclase
F: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,01910
Polymers63,2853
Non-polymers7347
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-62 kcal/mol
Surface area21090 Å2
MethodPISA
3
G: Allene oxide cyclase
H: Allene oxide cyclase
I: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,97310
Polymers63,2853
Non-polymers6887
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-83 kcal/mol
Surface area21210 Å2
MethodPISA
4
J: Allene oxide cyclase
K: Allene oxide cyclase
L: Allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6657
Polymers63,2853
Non-polymers3804
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-73 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.321, 67.430, 161.775
Angle α, β, γ (deg.)84.610, 79.320, 61.990
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


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


Mass: 18.015 Da / Num. of mol.: 2591 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / 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 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: 1.35→19.8 Å / Num. all: 446841 / Num. obs: 446841 / % possible obs: 82.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 22.825 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 15.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.35-1.450.4172.21326798287579.3
1.45-1.550.2323.891132786916887.1
1.55-1.750.1028.041585439495186.8
1.75-2.830.02424.8227332815751982.8
2.83-3.370.01641.74337481849277.1
3.37-3.910.01548.4417111924973.9
3.91-4.450.01350.629365504469.8
4.45-140.01256.8718078946064.6
14-170.0160.941226328.1
17-200.01559.94382021.1
20

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DIO

2dio


Resolution: 1.35→19.8 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1748 / WRfactor Rwork: 0.1372 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8749 / SU R Cruickshank DPI: 0.0567 / SU Rfree: 0.0548 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.057 / ESU R Free: 0.055 / 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
Rfree0.1741 22345 5 %thin shells (NCS)
Rwork0.1378 ---
obs0.1396 424547 82.39 %-
all-446841 --
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 max: 83.65 Å2 / Biso mean: 27.2248 Å2 / Biso min: 8.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20.34 Å20.01 Å2
2--0.33 Å2-0.86 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16577 0 133 2591 19301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217505
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.97623821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25852176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.5924.042762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.417152662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1061548
X-RAY DIFFRACTIONr_chiral_restr0.1070.22497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113644
X-RAY DIFFRACTIONr_rigid_bond_restr4.104317505
X-RAY DIFFRACTIONr_sphericity_free32.95252594
X-RAY DIFFRACTIONr_sphericity_bonded18.593516994
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 1343 -
Rwork0.248 25508 -
all-26851 -
obs--67.17 %

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