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- PDB-8pa2: Crystal structure of alcohol dehydrogenase/ketoreductase variant ... -

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Basic information

Entry
Database: PDB / ID: 8pa2
TitleCrystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form
ComponentsOxidoreductase, short-chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / ketoreductase / Short chain dehydrogenase
Function / homologyoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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 domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, short-chain dehydrogenase/reductase family
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRozeboom, H.J. / Janssen, D.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form
Authors: Delgado-Arciniega, E. / Bodescu, V. / Rozeboom, H.J. / Janssen, D.B. / Wijma, H.J.
History
DepositionJun 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, short-chain dehydrogenase/reductase family
B: Oxidoreductase, short-chain dehydrogenase/reductase family
C: Oxidoreductase, short-chain dehydrogenase/reductase family
D: Oxidoreductase, short-chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,83012
Polymers112,6184
Non-polymers3,2128
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, & gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18660 Å2
ΔGint-128 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.981, 92.937, 79.601
Angle α, β, γ (deg.)90.00, 107.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Oxidoreductase, short-chain dehydrogenase/reductase family


Mass: 28154.467 Da / Num. of mol.: 4
Mutation: V126P, G128P, V137Y, Q138L, A181F, V187L, A190L, Q204M, M245L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0369 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SLC4
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 20 % PEG3350, 0.1 M ammonium sulfate, 0.1M bis-tris propane pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.1→46.5 Å / Num. obs: 55663 / % possible obs: 97 % / Redundancy: 2.8 % / CC1/2: 0.973 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.044 / Rrim(I) all: 0.075 / Χ2: 0.47 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 99 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.321 / Num. measured all: 13695 / Num. unique obs: 4646 / CC1/2: 0.847 / Rpim(I) all: 0.22 / Rrim(I) all: 0.391 / Χ2: 0.4 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.5 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.58 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21511 2752 4.9 %RANDOM
Rwork0.17837 ---
obs0.18023 52871 96.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.424 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20.32 Å2
2--1.81 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7416 0 213 367 7996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137753
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157642
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.64110536
X-RAY DIFFRACTIONr_angle_other_deg1.3061.57317471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25720400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.284151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7211584
X-RAY DIFFRACTIONr_chiral_restr0.070.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021771
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5043.1363976
X-RAY DIFFRACTIONr_mcbond_other2.5033.1363975
X-RAY DIFFRACTIONr_mcangle_it3.7674.6954963
X-RAY DIFFRACTIONr_mcangle_other3.7674.6964964
X-RAY DIFFRACTIONr_scbond_it3.2643.6743777
X-RAY DIFFRACTIONr_scbond_other3.2643.6733778
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0515.3265574
X-RAY DIFFRACTIONr_long_range_B_refined7.06339.0658412
X-RAY DIFFRACTIONr_long_range_B_other7.05538.938352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A76320.07
12B76320.07
21A77080.05
22C77080.05
31A76980.07
32D76980.07
41B75980.07
42C75980.07
51B76720.06
52D76720.06
61C76480.06
62D76480.06
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 209 -
Rwork0.218 3972 -
obs--98.94 %

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