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- PDB-2j5g: The Native structure of a beta-Diketone Hydrolase from the Cyanob... -

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Basic information

Entry
Database: PDB / ID: 2j5g
TitleThe Native structure of a beta-Diketone Hydrolase from the Cyanobacterium Anabaena sp. PCC 7120
Components(ALR4455 PROTEIN) x 2
KeywordsHYDROLASE / ENZYME EVOLUTION / C-C BOND HYDROLASE / LYASE / CROTONASE / BIOCATALYSIS / BETA-DIKETONE
Function / homologyEnoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta / Alr4455 protein
Function and homology information
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBennett, J.P. / Whittingham, J.L. / Brzozowski, A.M. / Leonard, P.M. / Grogan, G.
CitationJournal: Biochemistry / Year: 2007
Title: Structural Characterisation of a Beta Diketone Hydrolase from the Cyanobacterium Anabaena Sp. Pcc 7120 in Native and Product Bound Forms, a Coenzyme A-Independent Member of the Crotonase Suprafamily
Authors: Bennett, J.P. / Whittingham, J.L. / Brzozowski, A.M. / Leonard, P.M. / Grogan, G.
History
DepositionSep 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALR4455 PROTEIN
B: ALR4455 PROTEIN
C: ALR4455 PROTEIN
D: ALR4455 PROTEIN
E: ALR4455 PROTEIN
F: ALR4455 PROTEIN
G: ALR4455 PROTEIN
H: ALR4455 PROTEIN
I: ALR4455 PROTEIN
J: ALR4455 PROTEIN
K: ALR4455 PROTEIN
L: ALR4455 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,20216
Polymers360,81712
Non-polymers3844
Water79,3744406
1
A: ALR4455 PROTEIN
B: ALR4455 PROTEIN
C: ALR4455 PROTEIN
D: ALR4455 PROTEIN
E: ALR4455 PROTEIN
F: ALR4455 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,6078
Polymers180,4156
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: ALR4455 PROTEIN
H: ALR4455 PROTEIN
I: ALR4455 PROTEIN
J: ALR4455 PROTEIN
K: ALR4455 PROTEIN
L: ALR4455 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,5948
Polymers180,4026
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.999, 83.188, 154.010
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ALR4455 PROTEIN / BETA-DIKETONE HYDROLASE


Mass: 30067.037 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7120 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8YNV6, beta-diketone hydrolase
#2: Protein ALR4455 PROTEIN / BETA-DIKETONE HYDROLASE


Mass: 30080.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7120 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8YNV6, beta-diketone hydrolase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4406 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE INCLUDES N-TERMINAL CLEAVABLE HIS TAG OF 6 HISTIDINE RESIDUES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 11

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growpH: 5.5
Details: 0.1 M MES PH 5.5, 15% PEG 4000, 0.8 M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 16, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 515541 / % possible obs: 97.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.26
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.71 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O8U

1o8u


Resolution: 1.46→154.3 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.938 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.177 25504 5 %RANDOM
Rwork0.15 ---
obs0.151 483592 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.24 Å2
2--0 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.46→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24022 0 20 4406 28448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02224873
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.95433882
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09253017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48823.7931239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87154192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.25315192
X-RAY DIFFRACTIONr_chiral_restr0.1020.23797
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219095
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.213216
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.217167
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.23746
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.2104
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.2124
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.515385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.302224253
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.096310816
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1084.59627
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 1777
Rwork0.197 34884

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