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- PDB-1tz2: Crystal structure of 1-aminocyclopropane-1-carboyxlate deaminase ... -

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Basic information

Entry
Database: PDB / ID: 1tz2
TitleCrystal structure of 1-aminocyclopropane-1-carboyxlate deaminase complexed with ACC
Components1-aminocyclopropane-1-carboxylate deaminase
KeywordsHYDROLASE / ACC / ACCD / PLP / Crystal / Complex / Substrate
Function / homology
Function and homology information


1-aminocyclopropane-1-carboxylate metabolic process / 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, bacterial / 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 / PYRIDOXAL-5'-PHOSPHATE / 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKarthikeyan, S. / Zhou, Q. / Zhao, Z. / Kao, C.L. / Tao, Z. / Robinson, H. / Liu, H.W. / Zhang, H.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Analysis of Pseudomonas 1-Aminocyclopropane-1-carboxylate Deaminase Complexes: Insight into the Mechanism of a Unique Pyridoxal-5'-phosphate Dependent Cyclopropane Ring-Opening Reaction
Authors: Karthikeyan, S. / Zhou, Q. / Zhao, Z. / Kao, C.L. / Tao, Z. / Robinson, H. / Liu, H.W. / Zhang, H.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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 / 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_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

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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)148,25212
Polymers146,8594
Non-polymers1,3938
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-31 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.702, 68.731, 351.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36714.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: ACP / Plasmid: PET17B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q00740, 1-aminocyclopropane-1-carboxylate deaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-1AC / 1-AMINOCYCLOPROPANECARBOXYLIC ACID


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


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / pH: 7.5
Details: ISOPROPANOL, PEG 4000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2002
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 95603 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.06 / Net I/σ(I): 21.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.472 / % possible all: 85.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TYZ

1tyz


Resolution: 2.1→44.59 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 236575.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4570 5 %RANDOM
Rwork0.213 ---
obs0.213 91183 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.96 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.89 Å20 Å20 Å2
2--2.26 Å20 Å2
3----7.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 88 581 10737
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 608 4.9 %
Rwork0.299 11708 -
obs--77.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLP_PATCH.PARPLP.TOP
X-RAY DIFFRACTION4ACC.PARACC.TOP

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