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- PDB-1zvc: X-ray structure of allene oxide cyclase from arabidopsis thaliana... -

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Basic information

Entry
Database: PDB / ID: 1zvc
TitleX-ray structure of allene oxide cyclase from arabidopsis thaliana AT3G25760
Componentsallene oxide cyclase
KeywordsISOMERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / AT3G25760 / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


allene-oxide cyclase / allene-oxide cyclase activity / jasmonic acid biosynthetic process / chloroplast envelope / chloroplast thylakoid membrane / chloroplast / cytosol
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
Allene oxide cyclase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Han, B.W. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-ray structure of allene oxide cyclase from arabidopsis thaliana AT3G25760
Authors: Center for Eukaryotic Structural Genomics (CESG)
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8762
Polymers20,8521
Non-polymers241
Water2,450136
1
A: allene oxide cyclase
hetero molecules

A: allene oxide cyclase
hetero molecules

A: allene oxide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6286
Polymers62,5553
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area5850 Å2
ΔGint-61 kcal/mol
Surface area19740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.191, 66.191, 212.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

MG

21A-282-

HOH

31A-296-

HOH

DetailsTHE BIOLOGICAL UNIT IS A TRIMER GENERATED BY 120 DEGREE ROTATION ABOUT THE CRYSTALLOGRAPHIC C-AXIS)

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Components

#1: Protein allene oxide cyclase /


Mass: 20851.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT3G25760 / Plasmid: PVP-27 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9LS03, allene-oxide cyclase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.4 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 297 K / pH: 6.5
Details: 10 mg/ml protein, 18.4% PEG 4K, 0.160 M POTASSIUM BROMIDE, 0.100 M BISTRIS, vapor diffusion, hanging drop, temperature 297K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.99997
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: WATER COOLED SI (111) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionRedundancy: 9.7 % / Number: 17352 / Rmerge(I) obs: 0.08 / Χ2: 1.398 / D res high: 1.79 Å / D res low: 50 Å / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.415098.710.0360.8289.3
3.54.4199.810.0641.2689.7
3.063.599.810.0861.6779.8
2.783.0699.610.0961.6159.7
2.582.7899.510.1041.5299.5
2.432.5899.710.1211.6359.5
2.312.4399.810.1281.5429.8
2.212.3199.810.1361.6859.5
2.122.2199.610.1511.6389.8
2.052.1299.710.1651.5889.7
1.982.0599.810.1851.5479.9
1.931.9899.710.211.35510
1.881.9310010.2491.15910.3
1.831.8810010.2781.03410.3
1.791.8396.710.310.8368.6
ReflectionResolution: 1.79→50 Å / Num. obs: 17352 / % possible obs: 99.5 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.62
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.212 / % possible all: 96.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.424 / Cor.coef. Fo:Fc: 0.617
Highest resolutionLowest resolution
Rotation4 Å35.45 Å
Translation4 Å35.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.6data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z8K

1z8k


Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.226 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.283 875 5.1 %RANDOM
Rwork0.236 ---
obs0.239 16437 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.46 Å20 Å2
2---0.93 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 1 136 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221375
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9881867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.59424.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30315223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.672154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2604
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7483871
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.86761371
X-RAY DIFFRACTIONr_scbond_it4.369570
X-RAY DIFFRACTIONr_scangle_it5.49812496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 69 -
Rwork0.346 1134 -
obs--95.48 %

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