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- PDB-5tcw: ACC oxidase complex with nickel and acetate -

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Basic information

Entry
Database: PDB / ID: 5tcw
TitleACC oxidase complex with nickel and acetate
Components1-aminocyclopropane-1-carboxylate oxidase 1
KeywordsOXIDOREDUCTASE / substrate complex / OXYGENASE
Function / homology
Function and homology information


aminocyclopropanecarboxylate oxidase / 1-aminocyclopropane-1-carboxylate oxidase activity / coumarin biosynthetic process / ethylene biosynthetic process / response to molecule of fungal origin / 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 ...: / 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
ACETATE ION / NICKEL (II) ION / 1-aminocyclopropane-1-carboxylate oxidase 1
Similarity search - Component
Biological speciesPetunia hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGunawardana, D.M. / Yosaatmadja, Y. / Leung, I.K. / Squire, C.J.
CitationJournal: To Be Published
Title: ACC oxidase complex with substrate 1-aminocyclopropane-1-carboxylic acid
Authors: Gunawardana, D.M. / Arabshahi, J. / Yosaatmadja, Y. / Reynisson, J. / Squire, C.J. / Leung, I.K.
History
DepositionSep 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)36,3513
Polymers36,2341
Non-polymers1182
Water00
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)145,40612
Polymers144,9354
Non-polymers4718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_558-x,y,-z+31
crystal symmetry operation4_558x,-y,-z+31
Buried area14630 Å2
ΔGint-103 kcal/mol
Surface area50090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.944, 108.136, 108.320
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 / ACCO / Ethylene-forming enzyme / EFE


Mass: 36233.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petunia hybrida (garden petunia) / Gene: ACO1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08506, aminocyclopropanecarboxylate oxidase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: sodium dihydrogen phosphate, lithium sulfate, potasium hydrogen phosphate. CAPS pH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→19.78 Å / Num. obs: 11727 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / CC1/2: 0.999 / Net I/σ(I): 18.1
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1 / CC1/2: 0.454 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WA6

1wa6


Resolution: 2.7→19.78 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.728 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R: 0.719 / ESU R Free: 0.341 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26944 597 5.1 %RANDOM
Rwork0.22476 ---
obs0.22705 11129 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.281 Å2
Baniso -1Baniso -2Baniso -3
1--4.21 Å2-0 Å2-0 Å2
2--3.42 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.7→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 5 0 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192404
X-RAY DIFFRACTIONr_bond_other_d0.0010.022275
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9733245
X-RAY DIFFRACTIONr_angle_other_deg0.81235252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1525.046109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25615416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.367159
X-RAY DIFFRACTIONr_chiral_restr0.0580.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
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_it2.0087.5581194
X-RAY DIFFRACTIONr_mcbond_other2.0057.561194
X-RAY DIFFRACTIONr_mcangle_it3.54111.331489
X-RAY DIFFRACTIONr_mcangle_other3.54111.331489
X-RAY DIFFRACTIONr_scbond_it1.7127.6991210
X-RAY DIFFRACTIONr_scbond_other1.7117.6991211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.02511.4691756
X-RAY DIFFRACTIONr_long_range_B_refined5.25458.3232535
X-RAY DIFFRACTIONr_long_range_B_other5.25458.332536
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 44 -
Rwork0.38 779 -
obs--96.94 %

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