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- PDB-9xax: Crystal structure of L-threonate 3-dehydrogenase from Paracoccus ... -

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Basic information

Entry
Database: PDB / ID: 9xax
TitleCrystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form)
ComponentsSDR family NAD(P)-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Short chain dihydrogenase/reductase superfamily
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TARTRONATE / SDR family NAD(P)-dependent oxidoreductase
Function and homology information
Biological speciesParacoccus litorisediminis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsWatanabe, S. / Sato, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Identification, functional characterization, and structural analysis of an atypical l-threonate 3-dehydrogenase.
Authors: Watanabe, S. / Sato, H. / Yokoi, T. / Terawaki, S.I.
History
DepositionOct 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SDR family NAD(P)-dependent oxidoreductase
B: SDR family NAD(P)-dependent oxidoreductase
C: SDR family NAD(P)-dependent oxidoreductase
D: SDR family NAD(P)-dependent oxidoreductase
E: SDR family NAD(P)-dependent oxidoreductase
F: SDR family NAD(P)-dependent oxidoreductase
G: SDR family NAD(P)-dependent oxidoreductase
H: SDR family NAD(P)-dependent oxidoreductase
I: SDR family NAD(P)-dependent oxidoreductase
J: SDR family NAD(P)-dependent oxidoreductase
K: SDR family NAD(P)-dependent oxidoreductase
L: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,73136
Polymers328,39412
Non-polymers10,33724
Water28,8061599
1
A: SDR family NAD(P)-dependent oxidoreductase
F: SDR family NAD(P)-dependent oxidoreductase
hetero molecules

I: SDR family NAD(P)-dependent oxidoreductase
J: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,91012
Polymers109,4654
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area20930 Å2
ΔGint-68 kcal/mol
Surface area28890 Å2
MethodPISA
2
B: SDR family NAD(P)-dependent oxidoreductase
E: SDR family NAD(P)-dependent oxidoreductase
G: SDR family NAD(P)-dependent oxidoreductase
K: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,91012
Polymers109,4654
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21050 Å2
ΔGint-64 kcal/mol
Surface area29190 Å2
MethodPISA
3
C: SDR family NAD(P)-dependent oxidoreductase
D: SDR family NAD(P)-dependent oxidoreductase
hetero molecules

H: SDR family NAD(P)-dependent oxidoreductase
L: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,91012
Polymers109,4654
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area21100 Å2
ΔGint-62 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.359, 72.552, 140.251
Angle α, β, γ (deg.)85.28, 82.57, 84.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SDR family NAD(P)-dependent oxidoreductase


Mass: 27366.127 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus litorisediminis (bacteria) / Gene: GL300_07955 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A844HLS7
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C21H28N7O17P3 / Source: (gene. exp.) Paracoccus litorisediminis (bacteria) / Production host: Escherichia coli DH5[alpha] (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TTN / TARTRONATE


Mass: 118.045 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1599 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 25% w/v PEG 3350, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→48.29 Å / Num. obs: 158234 / % possible obs: 97.8 % / Redundancy: 5.8 % / CC1/2: 0.859 / Net I/σ(I): 16.3
Reflection shellResolution: 2.08→2.12 Å / Mean I/σ(I) obs: 9.1 / Num. unique obs: 10418 / CC1/2: 0.314

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→48.29 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 7932 5.07 %
Rwork0.1686 --
obs0.1703 156586 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20892 0 672 1599 23163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421962
X-RAY DIFFRACTIONf_angle_d0.7530068
X-RAY DIFFRACTIONf_dihedral_angle_d11.9647642
X-RAY DIFFRACTIONf_chiral_restr0.0493499
X-RAY DIFFRACTIONf_plane_restr0.0063897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.10.21372600.16574916X-RAY DIFFRACTION95
2.1-2.130.2172920.16794830X-RAY DIFFRACTION96
2.13-2.150.25272440.16424924X-RAY DIFFRACTION96
2.15-2.180.22782780.1644938X-RAY DIFFRACTION96
2.18-2.210.22772760.16694847X-RAY DIFFRACTION96
2.21-2.240.23082660.17034951X-RAY DIFFRACTION96
2.24-2.270.23212360.16594905X-RAY DIFFRACTION96
2.27-2.310.19892690.16884899X-RAY DIFFRACTION96
2.31-2.340.22032630.16554957X-RAY DIFFRACTION96
2.34-2.380.2382420.17824920X-RAY DIFFRACTION95
2.38-2.420.252670.1764914X-RAY DIFFRACTION96
2.42-2.470.21672600.17384862X-RAY DIFFRACTION96
2.47-2.510.23962660.16894903X-RAY DIFFRACTION96
2.51-2.560.19522580.16384940X-RAY DIFFRACTION96
2.56-2.620.2192280.17284933X-RAY DIFFRACTION96
2.62-2.680.21152490.18124982X-RAY DIFFRACTION96
2.68-2.750.21522590.1864854X-RAY DIFFRACTION96
2.75-2.820.21662580.18394922X-RAY DIFFRACTION97
2.82-2.910.23852760.19285007X-RAY DIFFRACTION97
2.91-30.23922650.19434952X-RAY DIFFRACTION97
3-3.110.20912660.18844955X-RAY DIFFRACTION97
3.11-3.230.23072790.20044950X-RAY DIFFRACTION97
3.23-3.380.22172560.18955046X-RAY DIFFRACTION98
3.38-3.560.20492340.17655072X-RAY DIFFRACTION99
3.56-3.780.16612700.15965073X-RAY DIFFRACTION98
3.78-4.070.17862640.15515045X-RAY DIFFRACTION99
4.07-4.480.14552810.13555007X-RAY DIFFRACTION99
4.48-5.130.13372790.12835038X-RAY DIFFRACTION99
5.13-6.460.17032880.16095075X-RAY DIFFRACTION99
6.46-48.290.14463030.15065037X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3793-0.10610.17390.6644-0.11920.6472-0.0322-0.03780.02620.0261-0.01550.0528-0.0914-0.11190.04380.0630.02410.01870.1139-0.00080.05340.3496-0.1305-1.1247
20.6777-0.0045-0.11380.75380.28040.5479-0.0114-0.0061-0.13410.0680.0306-0.04890.12140.01070.00530.07680.01150.00660.03730.00820.0803-19.8589-10.8131-45.5688
30.53790.030.0540.76020.00190.74170.03270.0097-0.13120.00540.0125-0.09840.17650.0974-0.00480.1430.0254-0.00280.03250.00220.0806-0.549111.6307-92.6404
40.7151-0.03470.24490.8083-0.09780.67130.05710.0591-0.0818-0.1421-0.00190.13210.179-0.109-0.01150.1177-0.0274-0.02030.04830.00450.0806-23.212220.9743-108.9095
50.61930.2612-0.00540.9660.24020.5736-0.0111-0.02720.1950.03250.00850.2347-0.1075-0.07720.00570.06050.02230.02470.04710.01040.1434-38.688626.6847-46.1398
60.5625-0.02280.13650.70360.07710.91670.02110.1696-0.0686-0.1123-0.04530.01870.1036-0.06340.03640.06950.01310.03330.1362-0.00060.0499.2296-23.4956-16.6244
70.53260.0593-0.06490.78140.11870.9396-0.0099-0.02370.04030.04660.0175-0.1013-0.07180.084-0.0160.0566-0.0026-0.00050.0541-0.00040.0677-11.429516.4063-37.9585
80.68480.0624-0.01390.7310.08290.6863-0.00380.04190.1509-0.05570.00240.0927-0.1112-0.08730.0050.08220.01370.01160.0430.02090.0985-26.8079-23.6587-97.4877
90.6116-0.12240.0470.79170.10570.8026-0.01730.0190.12520.10560.0018-0.1211-0.11120.1072-0.02770.0741-0.03780.00920.09440.04030.0765-41.5511.531611.1666
100.6708-0.16080.28410.58660.07890.75150.01680.1048-0.03990.0336-0.0431-0.10480.18110.2295-0.00320.04960.05360.02090.15740.04490.0967-35.26-24.9771-0.0624
110.83010.21290.02680.71240.32270.7441-0.03960.1064-0.0109-0.0888-0.00260.14470.0818-0.1265-0.00080.0509-0.0187-0.00210.08690.00320.0812-44.57680.5342-58.3226
120.6143-0.16820.03091.06040.09470.8264-0.0606-0.10110.03680.20290.0755-0.14060.03350.0203-0.020.10.0136-0.01190.0345-0.01570.0545-8.3749-34.9407-77.155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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