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- PDB-8wwe: Crystal structure of (R)-DHPS dehydrogenase HpsN from Ruegeria po... -

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Basic information

Entry
Database: PDB / ID: 8wwe
TitleCrystal structure of (R)-DHPS dehydrogenase HpsN from Ruegeria pomeroyi DSS-3
Components(R)-DHPS dehydrogenase
KeywordsOXIDOREDUCTASE / NAD-dependent
Function / homology
Function and homology information


sulfopropanediol 3-dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding / cytosol
Similarity search - Function
Sulfopropanediol 3-dehydrogenase / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Sulfopropanediol 3-dehydrogenase
Similarity search - Component
Biological speciesRuegeria pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, L. / Tang, K.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92251306 China
Other government2020YFA0608300 China
National Natural Science Foundation of China (NSFC)4288102 China
National Natural Science Foundation of China (NSFC)42276120 China
Other government121311KYSB20190029 China
CitationJournal: Isme J / Year: 2024
Title: Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria.
Authors: Liu, L. / Gao, X. / Dong, C. / Wang, H. / Chen, X. / Ma, X. / Liu, S. / Chen, Q. / Lin, D. / Jiao, N. / Tang, K.
History
DepositionOct 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (R)-DHPS dehydrogenase
B: (R)-DHPS dehydrogenase
C: (R)-DHPS dehydrogenase
D: (R)-DHPS dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,1079
Polymers174,6274
Non-polymers4805
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-111 kcal/mol
Surface area63600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.045, 122.865, 210.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-501-

SO4

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Components

#1: Protein
(R)-DHPS dehydrogenase


Mass: 43656.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) / Strain: DSS-3 / Gene: hpsN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LVV1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
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: 2.52 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.1M ammonium sulfate, 0.1M tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→46.2 Å / Num. obs: 39957 / % possible obs: 99.4 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 20.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 1.191 / Num. unique obs: 3932 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIX1.18.1_3865refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.2 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 1511 3.8 %
Rwork0.2416 --
obs0.243 39749 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11125 0 25 0 11150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511345
X-RAY DIFFRACTIONf_angle_d1.84315407
X-RAY DIFFRACTIONf_dihedral_angle_d19.4551579
X-RAY DIFFRACTIONf_chiral_restr0.1151780
X-RAY DIFFRACTIONf_plane_restr0.0111979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.39881350.35083440X-RAY DIFFRACTION100
2.99-3.10.40461370.30843441X-RAY DIFFRACTION100
3.1-3.220.32811360.27373435X-RAY DIFFRACTION100
3.22-3.370.311370.26963438X-RAY DIFFRACTION100
3.37-3.550.37281360.28413455X-RAY DIFFRACTION100
3.55-3.770.41311280.37883304X-RAY DIFFRACTION95
3.77-4.060.26371370.23783463X-RAY DIFFRACTION100
4.06-4.470.20561380.19043488X-RAY DIFFRACTION100
4.47-5.120.22741390.17183504X-RAY DIFFRACTION100
5.12-6.440.25511410.21883563X-RAY DIFFRACTION100

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