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- PDB-1f2d: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE -

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Basic information

Entry
Database: PDB / ID: 1f2d
Title1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
Components1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
KeywordsLYASE / 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE / CARBON-CARBON LYASE / OPEN TWISTED ALPHA/BETA
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
PYRIDOXAL-5'-PHOSPHATE / 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesWilliopsis saturnus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsYao, M. / Ose, T. / Sugimoto, H. / Horiuchi, A. / Nakagawa, A. / Yokoi, D. / Murakami, T. / Honma, M. / Wakatsuki, S. / Tanaka, I.
CitationJournal: 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
DepositionMay 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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
D: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,72112
Polymers148,3494
Non-polymers1,3738
Water16,916939
1
A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
B: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8616
Polymers74,1742
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-64 kcal/mol
Surface area23390 Å2
MethodPISA
2
C: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
D: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8616
Polymers74,1742
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-65 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.38, 269.37, 186.62
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE


Mass: 37087.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Williopsis saturnus (fungus) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: Q7M523, EC: 4.1.99.4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, PYRIDOXAL 5'-PHOSPHATE, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 10 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 110515 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 9.05 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.39 / % possible all: 96.3
Reflection
*PLUS
Num. obs: 110126 / Redundancy: 9.08 % / Num. measured all: 1000373
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→15 Å / Isotropic thermal model: RESTRAINTS / Cross valid method: THROUGHT REFINEMENT / σ(F): 3.4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 10211 9.8 %9.8
Rwork0.221 ---
obs0.221 101968 90.38 %-
all-110358 --
Solvent computationSolvent model: THROUGHOUT REFINEMENT / Bsol: 60.1 Å2 / ksol: 0.4825 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.314 Å20 Å20 Å2
2---4.833 Å20 Å2
3---7.147 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-6.26 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10428 0 80 939 11447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
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_deg1.448
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.795
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it1.5
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2→2.01 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.33 -
Rwork0.289 547
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.256
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.795

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