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- PDB-8r0d: Crystal structure of Borneoldehydrogenase ancestor N39 -

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Basic information

Entry
Database: PDB / ID: 8r0d
TitleCrystal structure of Borneoldehydrogenase ancestor N39
ComponentsBorneoldehydrogenase
KeywordsOXIDOREDUCTASE / TERPENOID / ALCOHOL / BORNEOL / ROSSMANN-LIKE FOLD
Function / homologyFORMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHelmer, C.P.O. / Dimos, N. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG 2473-1 Germany
CitationJournal: To Be Published
Title: Crystal structure of Borneoldehydrogenase N39
Authors: Helmer, C.P.O. / Dimos, N. / Loll, B.
History
DepositionOct 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Borneoldehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1419
Polymers29,6601
Non-polymers4818
Water2,774154
1
A: Borneoldehydrogenase
hetero molecules

A: Borneoldehydrogenase
hetero molecules

A: Borneoldehydrogenase
hetero molecules

A: Borneoldehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,56236
Polymers118,6404
Non-polymers1,92232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)62.890, 85.520, 109.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Borneoldehydrogenase


Mass: 29660.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES/NaOH pH 7.4, 11% (w/v) PEG 3,000 / PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 138314 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 26.16 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.168 / Net I/σ(I): 16.8
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 21199 / CC1/2: 0.497 / Rrim(I) all: 1.446 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.76 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8184
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2099 1281 5 %
Rwork0.1746 24333 -
obs0.1764 25614 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 31 154 2003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022001
X-RAY DIFFRACTIONf_angle_d1.01482708
X-RAY DIFFRACTIONf_chiral_restr0.072318
X-RAY DIFFRACTIONf_plane_restr0.0075353
X-RAY DIFFRACTIONf_dihedral_angle_d13.2428726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.40441400.32932648X-RAY DIFFRACTION98.76
1.92-2.010.38021410.26882674X-RAY DIFFRACTION99.54
2.01-2.120.2741390.22462660X-RAY DIFFRACTION99.57
2.12-2.250.22251420.18662693X-RAY DIFFRACTION99.89
2.25-2.420.23181410.17482675X-RAY DIFFRACTION99.96
2.42-2.670.22621420.16992700X-RAY DIFFRACTION100
2.67-3.050.21541430.16032713X-RAY DIFFRACTION99.9
3.05-3.840.15731440.14912730X-RAY DIFFRACTION99.93
3.85-42.760.1771490.15482840X-RAY DIFFRACTION99.2

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