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- PDB-2j5s: Structural of ABDH, a beta-diketone hydrolase from the Cyanobacte... -

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Basic information

Entry
Database: PDB / ID: 2j5s
TitleStructural of ABDH, a beta-diketone hydrolase from the Cyanobacterium Anabaena sp. PCC 7120 bound to (S)-3-oxocyclohexyl acetic acid
ComponentsBETA-DIKETONE HYDROLASE
KeywordsHYDROLASE / ENZYME EVOLUTION / C-C BOND HYDROLASE / LYASE / CROTONASE / BIOCATALYSIS / BETA-DIKETONE
Function / homology
Function and homology information


Enoyl-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
Similarity search - Domain/homology
(S)-CYCLOHEXANONE-2-ACETATE / NICKEL (II) ION / Alr4455 protein
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-DIKETONE HYDROLASE
B: BETA-DIKETONE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5646
Polymers60,1342
Non-polymers4304
Water8,827490
1
A: BETA-DIKETONE HYDROLASE
B: BETA-DIKETONE HYDROLASE
hetero molecules

A: BETA-DIKETONE HYDROLASE
B: BETA-DIKETONE HYDROLASE
hetero molecules

A: BETA-DIKETONE HYDROLASE
B: BETA-DIKETONE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,69118
Polymers180,4026
Non-polymers1,28912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.387, 80.387, 125.882
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1254-

NI

21B-1254-

NI

31A-2064-

HOH

41A-2222-

HOH

51A-2224-

HOH

61B-2043-

HOH

71B-2107-

HOH

81B-2221-

HOH

91B-2222-

HOH

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Components

#1: Protein BETA-DIKETONE HYDROLASE


Mass: 30067.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PROTEIN WAS CO-CRYSTALLISED WITH SUBSTRATE / 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: Chemical ChemComp-KTA / (S)-CYCLOHEXANONE-2-ACETATE


Mass: 156.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12O3
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONTAINS N-TERMINAL CLEAVABLE HIS TAG OF SIX HISTIDINE RESIDUES.

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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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growpH: 7.5
Details: 0.1 M BIS-TRIS PROPANE PH 7.5, 20% PEG 3350, 0.2 M SODIUM MALONATE, 0.01 M BICYCLO[2.2.2]OCTANE-2,6-DIONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07
DetectorType: ADSC CCD / Detector: CCD / Date: May 20, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.57→40.19 Å / Num. obs: 64435 / % possible obs: 98.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.04
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.93 / % possible all: 89.9

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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: 1.57→40.19 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.227 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17 3228 5.1 %RANDOM
Rwork0.138 ---
obs0.14 60411 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: 14.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.57→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 24 490 4530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9595884
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76823.832214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80615727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.641534
X-RAY DIFFRACTIONr_chiral_restr0.1060.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.22177
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22967
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2405
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.2150
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7921.52637
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14624193
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75531880
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5424.51680
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: 1.57→1.61 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 200
Rwork0.212 3922

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