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- PDB-6m5n: Apo-Form Structure of Borneol Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6m5n
TitleApo-Form Structure of Borneol Dehydrogenase
ComponentsBorneol dehydrogenase
KeywordsOXIDOREDUCTASE / terpenoid / alcohol
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Borneol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. TCU-HL1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKhine, A.A. / Huang, K.F. / Ko, T.P. / Chen, H.P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural characterization of borneol dehydrogenase from Pseudomonas sp. TCU-HL1
Authors: Khine, A.A. / Huang, K.F. / Ko, T.P. / Chen, H.P.
History
DepositionMar 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Borneol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9095
Polymers27,6351
Non-polymers2734
Water5,134285
1
A: Borneol dehydrogenase
hetero molecules

A: Borneol dehydrogenase
hetero molecules

A: Borneol dehydrogenase
hetero molecules

A: Borneol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,63520
Polymers110,5424
Non-polymers1,09316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area16890 Å2
ΔGint-130 kcal/mol
Surface area36170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.629, 96.507, 142.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-304-

ACT

21A-304-

ACT

31A-401-

HOH

41A-466-

HOH

51A-575-

HOH

61A-620-

HOH

71A-636-

HOH

81A-650-

HOH

91A-685-

HOH

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Components

#1: Protein Borneol dehydrogenase


Mass: 27635.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. TCU-HL1 (bacteria) / Gene: THL1_4180 / Plasmid: pET-30a / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: A0A1B3EB36
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: PEG 8000, sodium acetate, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 21642 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 20.51 Å2 / CC1/2: 0.918 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.067 / Net I/σ(I): 11.54
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 5 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2120 / CC1/2: 0.679 / Rpim(I) all: 0.413 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3ak4

3ak4


Resolution: 1.84→25.55 Å / SU ML: 0.1878 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.2282
RfactorNum. reflection% reflection
Rfree0.1815 1076 5 %
Rwork0.1569 --
obs0.1581 21527 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.62 Å2
Refinement stepCycle: LAST / Resolution: 1.84→25.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 285 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051975
X-RAY DIFFRACTIONf_angle_d0.95712677
X-RAY DIFFRACTIONf_chiral_restr0.0613301
X-RAY DIFFRACTIONf_plane_restr0.0063355
X-RAY DIFFRACTIONf_dihedral_angle_d12.05281167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.920.26511280.22492436X-RAY DIFFRACTION96.21
1.92-2.020.26871320.19092506X-RAY DIFFRACTION99.32
2.02-2.150.20681360.17882581X-RAY DIFFRACTION100
2.15-2.320.19371330.16652539X-RAY DIFFRACTION100
2.32-2.550.1991350.16122557X-RAY DIFFRACTION100
2.55-2.920.19671350.15962555X-RAY DIFFRACTION100
2.92-3.670.16531360.14272603X-RAY DIFFRACTION100
3.67-25.550.13771410.13682674X-RAY DIFFRACTION99.79

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