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- PDB-7wwx: Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehyd... -

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Entry
Database: PDB / ID: 7wwx
TitleCrystal structure of Herbaspirillum huttiense L-arabinose 1-dehydrogenase (NAD bound form)
ComponentsNAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
KeywordsOXIDOREDUCTASE / L-ARABINOSE METABOLISM / NAD-DEPENDENT DEHYDROGENASE / SDR PROTEIN FAMILY
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesHerbaspirillum huttiense subsp. putei IAM 15032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsMatsubara, R. / Yoshiwara, K. / Watanabe, Y. / Watanabe, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein.
Authors: Watanabe, S. / Yoshiwara, K. / Matsubara, R. / Watanabe, Y.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
B: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8685
Polymers59,4352
Non-polymers1,4333
Water9,908550
1
A: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
B: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
hetero molecules

A: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
B: NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,73610
Polymers118,8714
Non-polymers2,8666
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19480 Å2
ΔGint-112 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.509, 83.562, 81.927
Angle α, β, γ (deg.)90.000, 113.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)


Mass: 29717.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum huttiense subsp. putei IAM 15032 (bacteria)
Gene: DFS02_4196 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A4R8JL46
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→42.82 Å / Num. obs: 114656 / % possible obs: 99.8 % / Redundancy: 9.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.079 / Rrim(I) all: 0.249 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.389.22.0325110855330.5760.7012.1541.697.9
7.45-42.7910.60.10477887360.9950.0340.10921.599.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NUG

3nug


Resolution: 1.36→42.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.979 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 5835 5.1 %RANDOM
Rwork0.1678 ---
obs0.1691 108813 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.82 Å2 / Biso mean: 12.04 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å2-0 Å2-0.3 Å2
2--0.05 Å20 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 1.36→42.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 95 550 4511
Biso mean--16.13 26.4 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134052
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173690
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.6335516
X-RAY DIFFRACTIONr_angle_other_deg1.6081.5748511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8521.884207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03215618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4781528
X-RAY DIFFRACTIONr_chiral_restr0.0980.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02886
LS refinement shellResolution: 1.36→1.395 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 459 -
Rwork0.284 7927 -
all-8386 -
obs--98.74 %

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