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- PDB-1j0a: Crystal Structure Analysis of the ACC deaminase homologue -

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Basic information

Entry
Database: PDB / ID: 1j0a
TitleCrystal Structure Analysis of the ACC deaminase homologue
Components1-aminocyclopropane-1-carboxylate deaminase
KeywordsLYASE / PLP dependent
Function / homology
Function and homology information


1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase activity
Similarity search - Function
D-cysteine desulfhydrase / 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
ISOPROPYL ALCOHOL / PYRIDOXAL-5'-PHOSPHATE / Putative 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsFujino, A. / Ose, T. / Honma, M. / Yao, M. / Tanaka, I.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii
Authors: Fujino, A. / Ose, T. / Yao, M. / Tokiwano, T. / Honma, M. / Watanabe, N. / 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: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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.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_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: 1-aminocyclopropane-1-carboxylate deaminase
B: 1-aminocyclopropane-1-carboxylate deaminase
C: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,78810
Polymers105,6983
Non-polymers1,0907
Water1,69394
1
A: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules

A: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2728
Polymers70,4662
Non-polymers8076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
2
B: 1-aminocyclopropane-1-carboxylate deaminase
C: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1526
Polymers70,4662
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-71 kcal/mol
Surface area23710 Å2
MethodPISA
3
A: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules

A: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules

B: 1-aminocyclopropane-1-carboxylate deaminase
C: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules

B: 1-aminocyclopropane-1-carboxylate deaminase
C: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,57620
Polymers211,3976
Non-polymers2,17914
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_565-x+y,-x+1,z+1/31
crystal symmetry operation6_655-x+1,-x+y,-z+2/31
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area23360 Å2
ΔGint-237 kcal/mol
Surface area62450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.340, 122.340, 115.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 35232.824 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O57809, EC: 4.1.99.4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: ammonium sulfate, 2-propanol, phosphate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 277 K / PH range low: 7 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.1 Msodium potassium phosphate1reservoirpH6.2-7.0
32.0 Mammonium sulfate1reservoir
43-8 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9792, 0.9795, 0.9640
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2001
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.9641
ReflectionResolution: 2.5→20 Å / Num. all: 34218 / Num. obs: 34168 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 51.58 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.067 / Net I/σ(I): 7.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4953 / Rsym value: 0.26 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 39 Å / Num. obs: 2668 / Num. measured all: 34161
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 98.6 % / Num. unique obs: 282 / Num. measured obs: 4953

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→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
Rfree0.2695 2759 -RANDOM
Rwork0.2012 ---
all-34194 --
obs-33228 97.2 %-
Displacement parametersBiso mean: 55.2873 Å2
Baniso -1Baniso -2Baniso -3
1-2.164 Å2-2.143 Å20 Å2
2--2.164 Å20 Å2
3----4.329 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7452 0 64 94 7610
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009681
X-RAY DIFFRACTIONc_angle_deg1.54243
X-RAY DIFFRACTIONc_dihedral_angle_d23.0174
X-RAY DIFFRACTIONc_improper_angle_d1.0257
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.374 238 -
Rwork0.2936 --
obs-2963 89.03 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.542
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.01
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.026

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