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- PDB-1w9y: The structure of ACC oxidase -

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Basic information

Entry
Database: PDB / ID: 1w9y
TitleThe structure of ACC oxidase
Components1-AMINOCYCLOPROPANE-1-CARBOXYLATE OXIDASE 1
KeywordsOXYGENASE / 2OG OXYGENASE / ACCO / ACC OXIDASE
Function / homology
Function and homology information


aminocyclopropanecarboxylate oxidase / 1-aminocyclopropane-1-carboxylate oxidase activity / coumarin biosynthetic process / response to molecule of fungal origin / ethylene biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / metal ion binding
Similarity search - Function
B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
1-aminocyclopropane-1-carboxylate oxidase 1
Similarity search - Component
Biological speciesPETUNIA HYBRIDA (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsZhang, Z. / Ren, J.-S. / Clifton, I.J. / Schofield, C.J.
CitationJournal: Chem.Biol. / Year: 2004
Title: Crystal Structure and Mechanistic Implications of 1-Aminocyclopropane-1-Carboxylic Acid Oxidase (the Ethyling Forming Enzyme)
Authors: Zhang, Z. / Ren, J.-S. / Clifton, I.J. / Schofield, C.J.
History
DepositionOct 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE OXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0332
Polymers36,9371
Non-polymers961
Water1,71195
1
A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE OXIDASE 1
hetero molecules

A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE OXIDASE 1
hetero molecules

A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE OXIDASE 1
hetero molecules

A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE OXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1338
Polymers147,7494
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.300, 107.930, 108.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein 1-AMINOCYCLOPROPANE-1-CARBOXYLATE OXIDASE 1 / ACC OXIDASE 1 / ETHYLENE-FORMING ENZYME / EFE


Mass: 36937.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PETUNIA HYBRIDA (garden petunia) / Plasmid: PICI0143 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08506, aminocyclopropanecarboxylate oxidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.96 Å3/Da / Density % sol: 58.11 %
Crystal growpH: 10.3
Details: 1.2 M SODIUM DIHYDROPHOSPHATE 0.6 M DIPOTASSIUM HYDROPHOSPHATE 0.3 M LITHIUM SULPHATE 0.1 M CAPS PH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 21, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.12→30 Å / Num. obs: 23601 / % possible obs: 98.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 35.6
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.82 / % possible all: 85.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→25 Å / Rfactor Rfree error: 0.0085 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: RESIDUES 267-274 AND 308-319 DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 1141 4.7 %RANDOM
Rwork0.2237 ---
obs0.2237 23600 96.8 %-
Solvent computationBsol: 75.6093 Å2 / ksol: 0.359788 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.071 Å20 Å20 Å2
2---7.875 Å20 Å2
3----3.196 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 5 95 2474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CYA.PAR
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5GW583011.PAR

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