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- PDB-1j0d: ACC deaminase mutant complexed with ACC -

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Basic information

Entry
Database: PDB / ID: 1j0d
TitleACC deaminase mutant complexed with ACC
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
Chem-5PA / 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesWilliopsis saturnus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 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: 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 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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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)149,5658
Polymers148,2364
Non-polymers1,3294
Water16,844935
1
A: 1-aminocyclopropane-1-carboxylate deaminase
B: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7834
Polymers74,1182
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-17 kcal/mol
Surface area23050 Å2
MethodPISA
2
C: 1-aminocyclopropane-1-carboxylate deaminase
D: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7834
Polymers74,1182
Non-polymers6642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-19 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.254, 267.293, 187.681
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 / ACCD / ACC deaminase


Mass: 37059.047 Da / Num. of mol.: 4 / Mutation: S1A, K51T
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, EC: 4.1.99.4
#2: Chemical
ChemComp-5PA / N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID / N-PYRIDOXYL-1-AMINO-CYCLOPROPANECARBOXYLIC ACID-5-MONOPHOSPHATE


Mass: 332.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ACC, 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: 2.2→63.2 Å / Num. all: 78434 / Num. obs: 76220 / % possible obs: 0.916 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 35.965 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10134 / Rsym value: 0.317 / % possible all: 84.1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 38 Å / % possible obs: 91.6 % / Num. measured all: 356148
Reflection shell
*PLUS
% possible obs: 84.1 % / Num. unique obs: 10134 / Num. measured obs: 45758

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1F2D

1f2d


Resolution: 2.2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 6024 8 %RANDOM
Rwork0.221 ---
all-82729 --
obs-75326 91.1 %-
Displacement parametersBiso mean: 38.7456 Å2
Baniso -1Baniso -2Baniso -3
1--0.787 Å20 Å20 Å2
2---2.995 Å20 Å2
3---3.782 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10420 0 88 935 11443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006734
X-RAY DIFFRACTIONc_angle_deg1.25917
X-RAY DIFFRACTIONc_dihedral_angle_d22.4112
X-RAY DIFFRACTIONc_improper_angle_d0.8257
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.3289 560 -
Rwork0.287 --
obs-6806 0.821 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 8 % / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4112
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8257

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