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- PDB-1tzj: Crystal Structure of 1-aminocyclopropane-1-carboxylate deaminase ... -

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Basic information

Entry
Database: PDB / ID: 1tzj
TitleCrystal Structure of 1-aminocyclopropane-1-carboxylate deaminase complexed with d-vinyl glycine
Components1-aminocyclopropane-1-carboxylate deaminase
KeywordsHYDROLASE / ACCD / substrate / PLP / Crystal / Complex
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
D-VINYLGLYCINE / PYRIDOXAL-5'-PHOSPHATE / 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 10, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
D: 1-aminocyclopropane-1-carboxylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,24212
Polymers146,8594
Non-polymers1,3838
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-90 kcal/mol
Surface area43040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.665, 68.425, 350.171
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-A3B / D-VINYLGLYCINE / 2-AMMONIOBUT-3-ENOATE / 2-AMINO-3-BUTENOATE


Mass: 101.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.85 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ISOPROPANOL, PEG 4000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2003 / Details: NULL
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 110952 / Num. obs: 110765 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 28.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 44.5
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 9.2 / Rsym value: 0.36 / % possible all: 99

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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: 1.99→29.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2775039.51 / 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
Rfree0.251 5544 5 %RANDOM
Rwork0.213 ---
all0.229 110952 --
obs0.213 110765 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6806 Å2 / ksol: 0.344591 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.33 Å20 Å20 Å2
2---1.58 Å20 Å2
3----3.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.99→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 84 527 10679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.99→2.11 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 826 5 %
Rwork0.291 15809 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PLP_PATCH.PARAMPLP.TOP
X-RAY DIFFRACTION5VIN.PARAMVIN.TOP

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