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- PDB-1j0e: ACC deaminase mutant reacton intermediate -

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Basic information

Entry
Database: PDB / ID: 1j0e
TitleACC deaminase mutant reacton intermediate
Components1-aminocyclopropane-1-carboxylate deaminase
KeywordsLYASE / PLP dependent B group
Function / homology
Function and homology information


amine catabolic process / 1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase activity / pyridoxal phosphate binding
Similarity search - Function
1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-AMINOCYCLOPROPANECARBOXYLIC ACID / 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesWilliopsis saturnus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsOse, T. / Fujino, A. / Yao, M. / Honma, M. / Tanaka, I.
Citation
Journal: J.BIOL.CHEM. / Year: 2003
Title: Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction
Authors: Ose, T. / Fujino, A. / Yao, M. / Watanabe, N. / Honma, M. / Tanaka, I.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus
Authors: Yao, M. / Ose, T. / Sugimoto, H. / Horiuchi, A. / Nakagawa, A. / Wakatsuki, S. / Yokoi, D. / Murakami, T. / Honma, M. / Tanaka, I.
History
DepositionNov 12, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref.db_code / _struct_ref.pdbx_align_begin

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-aminocyclopropane-1-carboxylate deaminase
B: 1-aminocyclopropane-1-carboxylate deaminase
C: 1-aminocyclopropane-1-carboxylate deaminase
D: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6018
Polymers149,1974
Non-polymers4044
Water16,916939
1
A: 1-aminocyclopropane-1-carboxylate deaminase
B: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8014
Polymers74,5982
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-13 kcal/mol
Surface area23210 Å2
MethodPISA
2
C: 1-aminocyclopropane-1-carboxylate deaminase
D: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8014
Polymers74,5982
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-16 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.400, 269.586, 186.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
1-aminocyclopropane-1-carboxylate deaminase / ACC deaminase / ACCD


Mass: 37299.242 Da / Num. of mol.: 4 / Mutation: S1A, Y295F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Williopsis saturnus (fungus) / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7M523, 1-aminocyclopropane-1-carboxylate deaminase
#2: Chemical
ChemComp-1AC / 1-AMINOCYCLOPROPANECARBOXYLIC ACID


Type: peptide linking / Mass: 101.104 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammmonium sulfate, pottasium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMACC1drop
215-20 mg/mlenzyme1drop
340 mMpotassium phosphate1droppH6.5
41 mMPLP1drop
55 %glycerol1drop
6100 mMpotassium phosphate1reservoirpH7.4-8.0
72.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→38.3 Å / Num. all: 63065 / Num. obs: 60876 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 41.575 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.068 / Net I/σ(I): 9.8
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.2 / Num. unique all: 8689 / Rsym value: 0.324 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 38 Å / Num. measured all: 302793
Reflection shell
*PLUS
% possible obs: 98.6 % / Num. unique obs: 8689 / Num. measured obs: 41102

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1F2D

1f2d


Resolution: 2.45→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 4786 -RANDOM
Rwork0.2022 ---
all-60277 --
obs-59904 99.4 %-
Displacement parametersBiso mean: 45.1457 Å2
Baniso -1Baniso -2Baniso -3
1-2.568 Å20 Å20 Å2
2---5.551 Å20 Å2
3---2.983 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10420 0 88 939 11447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006528
X-RAY DIFFRACTIONc_angle_d1.2603
X-RAY DIFFRACTIONc_dihedral_angle_d21.9988
X-RAY DIFFRACTIONc_improper_angle_d0.81763
LS refinement shellResolution: 2.45→2.54 Å
RfactorNum. reflection% reflection
Rfree0.2777 490 -
Rwork0.3369 --
obs-10261 0.9811 %
Refinement
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 38 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9988
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81763

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